├── LICENSE ├── README.md ├── contamination └── Hsapiens_Mmusculus │ ├── Hsapiens_Mmusculus_1.fq.gz │ ├── Hsapiens_Mmusculus_2.fq.gz │ └── README.md ├── flowcell ├── Config │ ├── HiSeqControlSoftware.Options.cfg │ ├── RTAStart.log │ ├── Variability_HiSeq_E.bin │ ├── hh5vtccxx_2015-10-05 16-22-05_Effective.cfg │ ├── hh5vtccxx_2015-10-05 16-22-05_Override.cfg │ └── hh5vtccxx_2015-10-05 16-22-05_SortedOverride.cfg ├── Data │ └── Intensities │ │ └── BaseCalls │ │ └── L001 │ │ ├── C1.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C10.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C100.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C101.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C102.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C103.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C104.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C105.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C106.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C107.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C108.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C109.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C11.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C110.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C111.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C112.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C113.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C114.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C115.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C116.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C117.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C118.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C119.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C12.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C120.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C121.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C122.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C123.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C124.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C125.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C126.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C127.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C128.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C129.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C13.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C130.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C131.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C132.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C133.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C134.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C135.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C136.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C137.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C138.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C139.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C14.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C140.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C141.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C142.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C143.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C144.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C145.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C146.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C147.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C148.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C149.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C15.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C150.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C151.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C152.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C153.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C154.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C155.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C156.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C157.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C158.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C159.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C16.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C160.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C161.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C162.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C163.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C164.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C165.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C166.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C167.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C168.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C169.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C17.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C170.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C171.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C172.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C173.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C174.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C175.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C176.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C177.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C178.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C179.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C18.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C180.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C181.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C182.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C183.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C184.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C185.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C186.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C187.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C188.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C189.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C19.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C190.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C191.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C192.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C193.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C194.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C195.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C196.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C197.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C198.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C199.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C2.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C20.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C200.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C201.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C202.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C203.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C204.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C205.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C206.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C207.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C208.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C209.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C21.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C210.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C211.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C212.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C213.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C214.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C215.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C216.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C217.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C218.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C219.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C22.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C220.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C221.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C222.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C223.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C224.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C225.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C226.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C227.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C228.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C229.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C23.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C230.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C231.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C232.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C233.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C234.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C235.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C236.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C237.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C238.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C239.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C24.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C240.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C241.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C242.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C243.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C244.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C245.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C246.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C247.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C248.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C249.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C25.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C250.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C251.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C252.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C253.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C254.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C255.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C256.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C257.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C258.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C259.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C26.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C260.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C261.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C262.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C263.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C264.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C265.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C266.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C267.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C268.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C269.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C27.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C270.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C271.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C272.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C273.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C274.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C275.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C276.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C277.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C278.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C279.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C28.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C280.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C281.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C282.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C283.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C284.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C285.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C286.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C287.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C288.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C289.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C29.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C290.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C291.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C292.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C293.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C294.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C295.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C296.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C297.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C298.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C299.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C3.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C30.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C300.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C301.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C302.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C31.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C32.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C33.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C34.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C35.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C36.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C37.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C38.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C39.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C4.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C40.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C41.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C42.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C43.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C44.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C45.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C46.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C47.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C48.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C49.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C5.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C50.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C51.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C52.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C53.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C54.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C55.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C56.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C57.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C58.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C59.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C6.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C60.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C61.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C62.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C63.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C64.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C65.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C66.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C67.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C68.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C69.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C7.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C70.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C71.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C72.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C73.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C74.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C75.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C76.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C77.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C78.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C79.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C8.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C80.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C81.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C82.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C83.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C84.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C85.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C86.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C87.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C88.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C89.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C9.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C90.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C91.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C92.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C93.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C94.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C95.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C96.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C97.1 │ │ └── s_1_1101.bcl.gz │ │ ├── C98.1 │ │ └── s_1_1101.bcl.gz │ │ └── C99.1 │ │ └── s_1_1101.bcl.gz ├── README.md ├── RTAComplete.txt ├── RTAConfiguration.xml ├── RTARead1Complete.txt ├── RTARead2Complete.txt ├── Recipe │ └── HH5VTCCXX.xml ├── RunInfo.xml ├── SampleSheet.csv ├── SequencingComplete.txt └── runParameters.xml ├── genomes ├── ERCC │ └── ERCC92 │ │ ├── bowtie2 │ │ ├── ERCC92.1.bt2 │ │ ├── ERCC92.2.bt2 │ │ ├── ERCC92.3.bt2 │ │ ├── ERCC92.4.bt2 │ │ ├── ERCC92.rev.1.bt2 │ │ └── ERCC92.rev.2.bt2 │ │ ├── meta │ │ ├── ERCC_Controls_Analysis.txt │ │ └── ERCC_Controls_Annotation.txt │ │ ├── rnaseq │ │ ├── ref-transcripts.gtf │ │ └── tophat │ │ │ ├── ERCC92.1.bt2 │ │ │ ├── ERCC92.2.bt2 │ │ │ ├── ERCC92.3.bt2 │ │ │ ├── ERCC92.4.bt2 │ │ │ ├── ERCC92.fa │ │ │ ├── ERCC92.fa.tlst │ │ │ ├── ERCC92.gff │ │ │ ├── ERCC92.rev.1.bt2 │ │ │ ├── ERCC92.rev.2.bt2 │ │ │ └── ERCC92.ver │ │ └── seq │ │ ├── ERCC92-resources.yaml │ │ └── ERCC92.fa ├── Hsapiens │ └── hg19 │ │ ├── bowtie2 │ │ ├── hg19.1.bt2 │ │ ├── hg19.2.bt2 │ │ ├── hg19.3.bt2 │ │ ├── hg19.4.bt2 │ │ ├── hg19.rev.1.bt2 │ │ └── hg19.rev.2.bt2 │ │ ├── bwa │ │ ├── hg19.fa.amb │ │ ├── hg19.fa.ann │ │ ├── hg19.fa.bwt │ │ ├── hg19.fa.pac │ │ └── hg19.fa.sa │ │ ├── rnaseq │ │ ├── ref-transcripts-mask.gtf │ │ ├── ref-transcripts.bed │ │ ├── ref-transcripts.gtf │ │ └── ref-transcripts.refflat │ │ ├── seq │ │ ├── hg19-resources.yaml │ │ ├── hg19.dict │ │ ├── hg19.fa │ │ └── hg19.fa.fai │ │ └── ucsc │ │ └── hg19.2bit └── Mmusculus │ └── mm9 │ ├── bowtie2 │ ├── mm9.1.bt2 │ ├── mm9.2.bt2 │ ├── mm9.3.bt2 │ ├── mm9.4.bt2 │ ├── mm9.rev.1.bt2 │ └── mm9.rev.2.bt2 │ ├── bwa │ ├── mm9.fa.amb │ ├── mm9.fa.ann │ ├── mm9.fa.bwt │ ├── mm9.fa.pac │ └── mm9.fa.sa │ ├── rnaseq │ ├── ref-transcripts-mask.gtf │ ├── ref-transcripts.gtf │ └── ref-transcripts.refFlat │ └── seq │ ├── mm9-resources.yaml │ ├── mm9.dict │ ├── mm9.fa │ └── mm9.fa.fai ├── rnaseq ├── Hsapiens │ ├── stranded │ │ ├── README.md │ │ ├── test_1.fq.gz │ │ └── test_2.fq.gz │ └── unstranded │ │ ├── Hsapiens_1.fq.gz │ │ ├── Hsapiens_2.fq.gz │ │ └── README └── Mmusculus │ └── unstranded │ ├── Mmusculus_1.fq.gz │ ├── Mmusculus_2.fq.gz │ ├── README │ └── align │ ├── Test1-ready.bai │ └── Test1-ready.bam ├── scripts ├── fastq_clip.py └── fastq_convert.py ├── vcf ├── README.md ├── sample1-bcbio-cancer.vcf ├── sample2-bcbio-cancer.vcf ├── spec-svs-v4.1.vcf └── spec-v4.3.vcf └── wgs ├── README.md ├── mt.bam ├── mt.parquet.adam ├── mt.sorted.bam ├── mt.sorted.bam.bai ├── mt_1.fq.gz └── mt_2.fq.gz /LICENSE: -------------------------------------------------------------------------------- 1 | The MIT License (MIT) 2 | 3 | Copyright (c) 2013 Rory Kirchner 4 | 5 | Permission is hereby granted, free of charge, to any person obtaining a copy of 6 | this software and associated documentation files (the "Software"), to deal in 7 | the Software without restriction, including without limitation the rights to 8 | use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of 9 | the Software, and to permit persons to whom the Software is furnished to do so, 10 | subject to the following conditions: 11 | 12 | The above copyright notice and this permission notice shall be included in all 13 | copies or substantial portions of the Software. 14 | 15 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 16 | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS 17 | FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR 18 | COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER 19 | IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN 20 | CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. 21 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | ##tiny-test-data 2 | Super small biological datasets designed with unit testing in mind. 3 | 4 | ###rationale 5 | Tests are great to have but they are not very fun to write and coming 6 | up with small datasets for testing, especially given the myriad of 7 | file formats we deal with, is often super annoying. One way to make 8 | tests less not-fun to write is to have a handy set of tiny test data 9 | at hand. 10 | 11 | ###contributing 12 | If you have a nice set of tiny test data of your own please open up a 13 | pull request. 14 | -------------------------------------------------------------------------------- /contamination/Hsapiens_Mmusculus/Hsapiens_Mmusculus_1.fq.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/roryk/tiny-test-data/4dc37f0aaf5b2f3eec260a91689effa4197bd2a3/contamination/Hsapiens_Mmusculus/Hsapiens_Mmusculus_1.fq.gz -------------------------------------------------------------------------------- /contamination/Hsapiens_Mmusculus/Hsapiens_Mmusculus_2.fq.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/roryk/tiny-test-data/4dc37f0aaf5b2f3eec260a91689effa4197bd2a3/contamination/Hsapiens_Mmusculus/Hsapiens_Mmusculus_2.fq.gz -------------------------------------------------------------------------------- /contamination/Hsapiens_Mmusculus/README.md: -------------------------------------------------------------------------------- 1 | These are files of 100 RNA-seq reads each, 80 of which come from human and 20 of which come from mouse. 2 | They are paired end reads run on the Illumina machines. They come from different experiments, taken from 3 | reads that map only to MT, so they have been adapter trimmed and quality controlled already. They are 4 | from a RNA-seq dataset but are useful for testing contamination detection in any NGS data. 5 | -------------------------------------------------------------------------------- /flowcell/Config/HiSeqControlSoftware.Options.cfg: -------------------------------------------------------------------------------- 1 | 2 | 3 | HighOutput 4 | true 5 | true 6 | true 7 | false 8 | ITF, Dynamic Focus, CV-Based 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 310 17 | 325 18 | 325 19 | true 20 | true 21 | false 22 | false 23 | {YY}{MM}{DD}_{SERIAL}_{RUN}_{FCPOS}{FCSERIAL} 24 | HiSeq Adapter Plate 25 | HiSeq Flow Cell Holder 26 | 27 | HiSeq X HD.bin 28 | HiSeq X HD.bin 29 | 30 | X:\wwcrc_genomics\hiseqx_data 31 | 32 | false 33 | Save All Thumbnails 34 | false 35 | 36 | 8081 37 | 8082 38 | 8080 39 | 288 40 | true 41 | false 42 | 600 43 | 44 | 45 | 8090 46 | 8091 47 | 48 | 49 | 50 | 51 | 52 | false 53 | false 54 | 300000 55 | true 56 | amqp://guest:guest@localhost:5672/ 57 | ILMNSequencerStatusUpdates 58 | 59 | 60 | false 61 | false 62 | true 63 | 64 | wwcrcgenomics@gmail.com 65 | 66 | 67 | 24 68 | 128 69 | C:\Illumina\SoftwareUpdates 70 | -------------------------------------------------------------------------------- /flowcell/Config/RTAStart.log: -------------------------------------------------------------------------------- 1 | title RTA 2.7.1 - O:\Illumina\HiSeqTemp\151005_ST-00295_0022_BHH5VTCCXX 2 | pushd "C:\Illumina\RTA" 3 | "C:\Illumina\RTA\RTA.exe" "O:\Illumina\HiSeqTemp\151005_ST-00295_0022_BHH5VTCCXX" outputfolder="X:\wwcrc_genomics\hiseqx_data" Processing.NumberOfThreads=24 configfile=C:\Illumina\RTA\Configs\HiSeqX.Configuration.xml Processing.WorkProviderServicePort=8082 ImageAnalysis.RigidRegistrationSecondOrderCoefficients="-1.8125E-07,-1.65625E-07,0,-6.25E-08,-2.015625E-07,0,6.375E-07,1.1875E-07,0,7.875E-07,-9.375E-08,0" ImageAnalysis.RigidRegistrationThirdOrderCoefficients="1.457467E-09,-3.208194E-07,-2.450433E-05,1.379342E-09,-4.036319E-07,3.143317E-05,1.551217E-09,-3.864444E-07,-1.575433E-05,1.551217E-09,-3.255069E-07,6.433172E-06" ImageAnalysis.UpperLeftFiducialXInPixels=1085 ImageAnalysis.UpperLeftFiducialYInPixels=1810 ImageAnalysis.RigidRegistrationPitchInPixels=2.03 ImageAnalysis.RigidRegistrationNumberOfColumns=507 ImageAnalysis.RigidRegistrationNumberOfRows=2063 -------------------------------------------------------------------------------- /flowcell/Config/Variability_HiSeq_E.bin: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/roryk/tiny-test-data/4dc37f0aaf5b2f3eec260a91689effa4197bd2a3/flowcell/Config/Variability_HiSeq_E.bin -------------------------------------------------------------------------------- /flowcell/Config/hh5vtccxx_2015-10-05 16-22-05_Override.cfg: -------------------------------------------------------------------------------- 1 | 2 | ; Override Version HiSeqX_1.6 3 | 4 | [_FileInfo] 5 | OverrideVersion = HiSeqX_1.6 10/20/2014 11:24 AM 6 | 7 | [system] 8 | ;AdvancedOptionsEnabled = true 9 | Name = ST-00295 ; *** Calibration *** *********** System Specific ************ 10 | InstrumentType = HiSeqX 11 | 12 | [Scanner.ChemistryModule] 13 | Exists = true 14 | Simulated = false 15 | 16 | [ChemistryModule] 17 | Exists = true 18 | Simulated = false 19 | 20 | [CameraFrameGrabber] 21 | Simulated = false 22 | 23 | [Camera1] 24 | Simulated = false 25 | 26 | [Camera2] 27 | Simulated = false 28 | 29 | [Compensator] 30 | Simulated = false 31 | GalvoInDAC = 100 32 | GalvoOutDAC = 115 33 | topsurfaceoffset = 0.0224 ; *** Calibration *** 34 | 35 | [fpga] 36 | Simulated = false 37 | 38 | [laser] 39 | LaserMeasuredOverSetPowerRatioForWarning = 0.0 ; never display laser warning 40 | LaserMeasuredOverSetPowerRatioForError = 0.0 ; never display error or stop run because of laser 41 | 42 | [LaserShutter] 43 | Simulated = false ; *** Calibration *** 44 | 45 | [SequencingLaser1] 46 | LaserPower = 1000 47 | Simulated = false ; *** Calibration *** Simulate until OP600 48 | 49 | [SequencingLaser2] 50 | LaserPower = 1200 51 | Simulated = false ; *** Calibration *** Simulate until OP600 52 | 53 | [SequencingExcitationFilter1] 54 | HomeOffsetSteps = 5 ; *** Calibration *** *********** System Specific ************ 55 | Simulated = false 56 | 57 | [SequencingExcitationFilter2] 58 | HomeOffsetSteps = -15 ; *** Calibration *** *********** System Specific ************ 59 | Simulated = false 60 | 61 | [EmissionFilter] 62 | Simulated = false 63 | 64 | [TiltMotor] 65 | Simulated = false 66 | 67 | [XMotor] 68 | Simulated = false 69 | 70 | [YMotor] 71 | Simulated = false 72 | 73 | [ZMotor] 74 | Simulated = false 75 | 76 | [autotilt_autocenter] 77 | AutoTiltLaser2Power = 200 ; *** Calibration *** 78 | Laser1Power = 1000 ; *** Calibration *** *********** System Specific ************ 79 | Laser2Power = 1200 ; *** Calibration *** *********** System Specific ************ 80 | MaxNumACRetries = 4 81 | 82 | [SecondOrderDistortionCorrection] 83 | ChannelACoeffA =-1.8125E-07 84 | ChannelACoeffB =-1.65625E-07 85 | ChannelACoeffC =0 86 | ChannelCCoeffA =-6.25E-08 87 | ChannelCCoeffB =-2.015625E-07 88 | ChannelCCoeffC =0 89 | ChannelGCoeffA =6.375E-07 90 | ChannelGCoeffB =1.1875E-07 91 | ChannelGCoeffC =0 92 | ChannelTCoeffA =7.875E-07 93 | ChannelTCoeffB =-9.375E-08 94 | ChannelTCoeffC =0 95 | 96 | [ThirdOrderDistortionCorrection] 97 | ChannelACoeffA =1.457467E-09 98 | ChannelACoeffB =-3.208194E-07 99 | ChannelACoeffC =-2.450433E-05 100 | ChannelCCoeffA =1.379342E-09 101 | ChannelCCoeffB =-4.036319E-07 102 | ChannelCCoeffC =3.143317E-05 103 | ChannelGCoeffA =1.551217E-09 104 | ChannelGCoeffB =-3.864444E-07 105 | ChannelGCoeffC =-1.575433E-05 106 | ChannelTCoeffA =1.551217E-09 107 | ChannelTCoeffB =-3.255069E-07 108 | ChannelTCoeffC =6.433172E-06 109 | 110 | [calibration/HiSeq Adapter Plate/HiSeq Flow Cell Holder] 111 | autoTiltExpectedFocus = -0.12 112 | zFocusOffsetForReflective = 0 113 | zFocusOffsetForEmmissive = 0 114 | XCorrection = 3.245 ; 3.268 ; *** Calibration *** 115 | YCorrection = -46.25 ; -46.166 ; *** Calibration *** 116 | XCorrection2 = 3.127 ; 3.162 ; *** Calibration *** 117 | YCorrection2 = -46.217 ; -46.08 ; *** Calibration *** 118 | NominalTilt1Correction = 0.63 ; *** Calibration *** 119 | NominalTilt2Correction = 0.53 ; *** Calibration *** 120 | NominalTilt3Correction = 0.8 ; *** Calibration *** 121 | NominalTilt1Correction_slide2 = 0.53 ; *** Calibration *** 122 | NominalTilt2Correction_slide2 = 0.62 ; *** Calibration *** 123 | NominalTilt3Correction_slide2 = 0.85 ; *** Calibration *** 124 | zFocusOffsetForEmmissiveTopSurface = 0 ; *** Calibration *** 125 | zFocusOffsetForEmmissiveBottomSurface = 0 ; *** Calibration *** 126 | RotationCorrection = 0 ; *** Calibration *** 127 | 128 | [calibration/HiSeq Adapter Plate/HiSeq Transposed BeadChip Holder] 129 | autoTiltExpectedFocus = -.12 130 | zFocusOffsetForReflective = 0 131 | zFocusOffsetForEmmissive = 0 132 | XCorrection = 3.245 ; 3.118 ; *** Calibration *** 133 | YCorrection = -46.25 ; -45.166 ; *** Calibration *** 134 | XCorrection2 = 3.127 ; 3.012 ; *** Calibration *** 135 | YCorrection2 = -46.217 ; -45.08 ; *** Calibration *** 136 | NominalTilt1Correction = 0.9351 ; *** Calibration *** 137 | NominalTilt2Correction = 0.8393 ; *** Calibration *** 138 | NominalTilt3Correction = 1.1045 ; *** Calibration *** 139 | NominalTilt1Correction_slide2 = 0.8396 ; *** Calibration *** 140 | NominalTilt2Correction_slide2 = 0.9216 ; *** Calibration *** 141 | NominalTilt3Correction_slide2 = 1.153 ; *** Calibration *** 142 | zFocusOffsetForEmmissiveTopSurface = 0 ; *** Calibration *** 143 | zFocusOffsetForEmmissiveBottomSurface = 0 ; *** Calibration *** 144 | RotationCorrection = 0 ; *** Calibration *** 145 | 146 | [scanner.chemistrymodule.arm9boardserialport] 147 | Reagent1RTD_Slope = 1 ; *** Calibration *** ****** System Specific ****** 148 | Reagent1RTD_Offset = 0 ; *** Calibration *** ****** System Specific ****** 149 | Reagent2RTD_Slope = 1 ; *** Calibration *** ****** System Specific ****** 150 | Reagent2RTD_Offset = 0 ; *** Calibration *** ****** System Specific ****** 151 | Reagent3RTD_Slope = 0.9933333 ; *** Calibration *** ****** System Specific ****** 152 | Reagent3RTD_Offset = 0.0333336 ; *** Calibration *** ****** System Specific ****** 153 | FlowCell1RTD_Slope = 0.9571428 ; *** Calibration *** ****** System Specific ****** 154 | FlowCell1RTD_Offset = 0.9571438 ; *** Calibration *** ****** System Specific ****** 155 | FlowCell2RTD_Slope = 0.9771428 ; *** Calibration *** ****** System Specific ****** 156 | FlowCell2RTD_Offset = 0.05714536 ; *** Calibration *** ****** System Specific ****** 157 | 158 | [PassiveDoor] 159 | Exists = true 160 | 161 | [EjectButton] 162 | Simulated = false 163 | 164 | [Drawer] 165 | Simulated = false 166 | 167 | [StageSafety] 168 | UndockedXPositiveRange = 47 ; *** Calibration *** ****** System Specific ****** 169 | UndockedYPositiveRange = -60 ; *** Calibration *** ****** System Specific ****** 170 | 171 | [xmotor_mdrive_5mm] 172 | neg_limit_mm = -59 ; *** Calibration *** ****** System Specific ****** 173 | pos_limit_mm = 36 ; *** Calibration *** ****** System Specific ****** 174 | 175 | [ymotor_copleyservo] 176 | pos_limit_mm = 73 ; *** Calibration *** ****** System Specific ****** 177 | 178 | [PEPrimingPump] 179 | Simulated = false 180 | 181 | [PEPriming] 182 | Simulated = false 183 | 184 | [ARM9PEPrimingBoardSerialPort] 185 | Simulated = false 186 | 187 | [Scanner.ChemistryModule.ARM9PEPrimingBoardSerialPort] 188 | Simulated = false 189 | 190 | [Scanner.ChemistryModule.FlowcellFluidics1.PEPriming] 191 | Simulated = false 192 | 193 | [Scanner.ChemistryModule.FlowcellFluidics2.PEPriming] 194 | Simulated = false 195 | 196 | [Scanner.ChemistryModule.FlowcellFluidics1.PEPriming.PEPrimingPump] 197 | Simulated = false 198 | 199 | [Scanner.ChemistryModule.FlowcellFluidics2.PEPriming.PEPrimingPump] 200 | Simulated = false 201 | 202 | [PEPrimingBypassValve] 203 | Simulated = false 204 | 205 | [Scanner.ChemistryModule.FlowcellFluidics1.PEPriming.PEPrimingBypassValve] 206 | Simulated = false 207 | 208 | [Scanner.ChemistryModule.FlowcellFluidics2.PEPriming.PEPrimingBypassValve] 209 | Simulated = false 210 | 211 | [PEPrimingWasteValve] 212 | Simulated = false 213 | 214 | [Scanner.ChemistryModule.FlowcellFluidics1.PEPriming.PEPrimingWasteValve] 215 | Simulated = false 216 | 217 | [Scanner.ChemistryModule.FlowcellFluidics2.PEPriming.PEPrimingWasteValve] 218 | Simulated = false 219 | -------------------------------------------------------------------------------- /flowcell/Config/hh5vtccxx_2015-10-05 16-22-05_SortedOverride.cfg: -------------------------------------------------------------------------------- 1 | ; d:\Archimedes_Flash\Override.cfg 2 | 3 | 4 | [_fileinfo] 5 | overrideversion = HiSeqX_1.6 10/20/2014 11:24 AM ; Override.cfg 6 | 7 | [arm9peprimingboardserialport] 8 | simulated = false ; Override.cfg 9 | 10 | [autotilt_autocenter] 11 | autotiltlaser2power = 200 ; Override.cfg 12 | laser1power = 1000 ; Override.cfg 13 | laser2power = 1200 ; Override.cfg 14 | maxnumacretries = 4 ; Override.cfg 15 | 16 | [calibration/hiseq adapter plate/hiseq flow cell holder] 17 | autotiltexpectedfocus = -0.12 ; Override.cfg 18 | nominaltilt1correction = 0.63 ; Override.cfg 19 | nominaltilt1correction_slide2 = 0.53 ; Override.cfg 20 | nominaltilt2correction = 0.53 ; Override.cfg 21 | nominaltilt2correction_slide2 = 0.62 ; Override.cfg 22 | nominaltilt3correction = 0.8 ; Override.cfg 23 | nominaltilt3correction_slide2 = 0.85 ; Override.cfg 24 | rotationcorrection = 0 ; Override.cfg 25 | xcorrection = 3.245 ; Override.cfg 26 | xcorrection2 = 3.127 ; Override.cfg 27 | ycorrection = -46.25 ; Override.cfg 28 | ycorrection2 = -46.217 ; Override.cfg 29 | zfocusoffsetforemmissive = 0 ; Override.cfg 30 | zfocusoffsetforemmissivebottomsurface = 0 ; Override.cfg 31 | zfocusoffsetforemmissivetopsurface = 0 ; Override.cfg 32 | zfocusoffsetforreflective = 0 ; Override.cfg 33 | 34 | [calibration/hiseq adapter plate/hiseq transposed beadchip holder] 35 | autotiltexpectedfocus = -.12 ; Override.cfg 36 | nominaltilt1correction = 0.9351 ; Override.cfg 37 | nominaltilt1correction_slide2 = 0.8396 ; Override.cfg 38 | nominaltilt2correction = 0.8393 ; Override.cfg 39 | nominaltilt2correction_slide2 = 0.9216 ; Override.cfg 40 | nominaltilt3correction = 1.1045 ; Override.cfg 41 | nominaltilt3correction_slide2 = 1.153 ; Override.cfg 42 | rotationcorrection = 0 ; Override.cfg 43 | xcorrection = 3.245 ; Override.cfg 44 | xcorrection2 = 3.127 ; Override.cfg 45 | ycorrection = -46.25 ; Override.cfg 46 | ycorrection2 = -46.217 ; Override.cfg 47 | zfocusoffsetforemmissive = 0 ; Override.cfg 48 | zfocusoffsetforemmissivebottomsurface = 0 ; Override.cfg 49 | zfocusoffsetforemmissivetopsurface = 0 ; Override.cfg 50 | zfocusoffsetforreflective = 0 ; Override.cfg 51 | 52 | [camera1] 53 | simulated = false ; Override.cfg 54 | 55 | [camera2] 56 | simulated = false ; Override.cfg 57 | 58 | [cameraframegrabber] 59 | simulated = false ; Override.cfg 60 | 61 | [chemistrymodule] 62 | exists = true ; Override.cfg 63 | simulated = false ; Override.cfg 64 | 65 | [compensator] 66 | galvoindac = 100 ; Override.cfg 67 | galvooutdac = 115 ; Override.cfg 68 | simulated = false ; Override.cfg 69 | topsurfaceoffset = 0.0224 ; Override.cfg 70 | 71 | [drawer] 72 | simulated = false ; Override.cfg 73 | 74 | [ejectbutton] 75 | simulated = false ; Override.cfg 76 | 77 | [emissionfilter] 78 | simulated = false ; Override.cfg 79 | 80 | [fpga] 81 | simulated = false ; Override.cfg 82 | 83 | [laser] 84 | lasermeasuredoversetpowerratioforerror = 0.0 ; Override.cfg 85 | lasermeasuredoversetpowerratioforwarning = 0.0 ; Override.cfg 86 | 87 | [lasershutter] 88 | simulated = false ; Override.cfg 89 | 90 | [passivedoor] 91 | exists = true ; Override.cfg 92 | 93 | [pepriming] 94 | simulated = false ; Override.cfg 95 | 96 | [peprimingbypassvalve] 97 | simulated = false ; Override.cfg 98 | 99 | [peprimingpump] 100 | simulated = false ; Override.cfg 101 | 102 | [peprimingwastevalve] 103 | simulated = false ; Override.cfg 104 | 105 | [scanner.chemistrymodule] 106 | exists = true ; Override.cfg 107 | simulated = false ; Override.cfg 108 | 109 | [scanner.chemistrymodule.arm9boardserialport] 110 | flowcell1rtd_offset = 0.9571438 ; Override.cfg 111 | flowcell1rtd_slope = 0.9571428 ; Override.cfg 112 | flowcell2rtd_offset = 0.05714536 ; Override.cfg 113 | flowcell2rtd_slope = 0.9771428 ; Override.cfg 114 | reagent1rtd_offset = 0 ; Override.cfg 115 | reagent1rtd_slope = 1 ; Override.cfg 116 | reagent2rtd_offset = 0 ; Override.cfg 117 | reagent2rtd_slope = 1 ; Override.cfg 118 | reagent3rtd_offset = 0.0333336 ; Override.cfg 119 | reagent3rtd_slope = 0.9933333 ; Override.cfg 120 | 121 | [scanner.chemistrymodule.arm9peprimingboardserialport] 122 | simulated = false ; Override.cfg 123 | 124 | [scanner.chemistrymodule.flowcellfluidics1.pepriming] 125 | simulated = false ; Override.cfg 126 | 127 | [scanner.chemistrymodule.flowcellfluidics1.pepriming.peprimingbypassvalve] 128 | simulated = false ; Override.cfg 129 | 130 | [scanner.chemistrymodule.flowcellfluidics1.pepriming.peprimingpump] 131 | simulated = false ; Override.cfg 132 | 133 | [scanner.chemistrymodule.flowcellfluidics1.pepriming.peprimingwastevalve] 134 | simulated = false ; Override.cfg 135 | 136 | [scanner.chemistrymodule.flowcellfluidics2.pepriming] 137 | simulated = false ; Override.cfg 138 | 139 | [scanner.chemistrymodule.flowcellfluidics2.pepriming.peprimingbypassvalve] 140 | simulated = false ; Override.cfg 141 | 142 | [scanner.chemistrymodule.flowcellfluidics2.pepriming.peprimingpump] 143 | simulated = false ; Override.cfg 144 | 145 | [scanner.chemistrymodule.flowcellfluidics2.pepriming.peprimingwastevalve] 146 | simulated = false ; Override.cfg 147 | 148 | [secondorderdistortioncorrection] 149 | channelacoeffa = -1.8125E-07 ; Override.cfg 150 | channelacoeffb = -1.65625E-07 ; Override.cfg 151 | channelacoeffc = 0 ; Override.cfg 152 | channelccoeffa = -6.25E-08 ; Override.cfg 153 | channelccoeffb = -2.015625E-07 ; Override.cfg 154 | channelccoeffc = 0 ; Override.cfg 155 | channelgcoeffa = 6.375E-07 ; Override.cfg 156 | channelgcoeffb = 1.1875E-07 ; Override.cfg 157 | channelgcoeffc = 0 ; Override.cfg 158 | channeltcoeffa = 7.875E-07 ; Override.cfg 159 | channeltcoeffb = -9.375E-08 ; Override.cfg 160 | channeltcoeffc = 0 ; Override.cfg 161 | 162 | [sequencingexcitationfilter1] 163 | homeoffsetsteps = 5 ; Override.cfg 164 | simulated = false ; Override.cfg 165 | 166 | [sequencingexcitationfilter2] 167 | homeoffsetsteps = -15 ; Override.cfg 168 | simulated = false ; Override.cfg 169 | 170 | [sequencinglaser1] 171 | laserpower = 1000 ; Override.cfg 172 | simulated = false ; Override.cfg 173 | 174 | [sequencinglaser2] 175 | laserpower = 1200 ; Override.cfg 176 | simulated = false ; Override.cfg 177 | 178 | [stagesafety] 179 | undockedxpositiverange = 47 ; Override.cfg 180 | undockedypositiverange = -60 ; Override.cfg 181 | 182 | [system] 183 | instrumenttype = HiSeqX ; Override.cfg 184 | name = ST-00295 ; Override.cfg 185 | 186 | [thirdorderdistortioncorrection] 187 | channelacoeffa = 1.457467E-09 ; Override.cfg 188 | channelacoeffb = -3.208194E-07 ; Override.cfg 189 | channelacoeffc = -2.450433E-05 ; Override.cfg 190 | channelccoeffa = 1.379342E-09 ; Override.cfg 191 | channelccoeffb = -4.036319E-07 ; Override.cfg 192 | channelccoeffc = 3.143317E-05 ; Override.cfg 193 | channelgcoeffa = 1.551217E-09 ; Override.cfg 194 | channelgcoeffb = -3.864444E-07 ; Override.cfg 195 | channelgcoeffc = -1.575433E-05 ; Override.cfg 196 | channeltcoeffa = 1.551217E-09 ; Override.cfg 197 | channeltcoeffb = -3.255069E-07 ; Override.cfg 198 | channeltcoeffc = 6.433172E-06 ; Override.cfg 199 | 200 | [tiltmotor] 201 | simulated = false ; Override.cfg 202 | 203 | [xmotor] 204 | simulated = false ; Override.cfg 205 | 206 | [xmotor_mdrive_5mm] 207 | neg_limit_mm = -59 ; Override.cfg 208 | pos_limit_mm = 36 ; Override.cfg 209 | 210 | [ymotor] 211 | simulated = false ; Override.cfg 212 | 213 | [ymotor_copleyservo] 214 | pos_limit_mm = 73 ; Override.cfg 215 | 216 | [zmotor] 217 | simulated = false ; Override.cfg 218 | 219 | 220 | -------------------------------------------------------------------------------- /flowcell/Data/Intensities/BaseCalls/L001/C1.1/s_1_1101.bcl.gz: -------------------------------------------------------------------------------- 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-------------------------------------------------------------------------------- 1 | ../C1.1/s_1_1101.bcl.gz -------------------------------------------------------------------------------- /flowcell/Data/Intensities/BaseCalls/L001/C95.1/s_1_1101.bcl.gz: -------------------------------------------------------------------------------- 1 | ../C1.1/s_1_1101.bcl.gz -------------------------------------------------------------------------------- /flowcell/Data/Intensities/BaseCalls/L001/C96.1/s_1_1101.bcl.gz: -------------------------------------------------------------------------------- 1 | ../C1.1/s_1_1101.bcl.gz -------------------------------------------------------------------------------- /flowcell/Data/Intensities/BaseCalls/L001/C97.1/s_1_1101.bcl.gz: -------------------------------------------------------------------------------- 1 | ../C1.1/s_1_1101.bcl.gz -------------------------------------------------------------------------------- /flowcell/Data/Intensities/BaseCalls/L001/C98.1/s_1_1101.bcl.gz: -------------------------------------------------------------------------------- 1 | ../C1.1/s_1_1101.bcl.gz -------------------------------------------------------------------------------- /flowcell/Data/Intensities/BaseCalls/L001/C99.1/s_1_1101.bcl.gz: -------------------------------------------------------------------------------- 1 | ../C1.1/s_1_1101.bcl.gz -------------------------------------------------------------------------------- /flowcell/README.md: -------------------------------------------------------------------------------- 1 | # Gold (trimmed) Flowcell for pipeline testing # 2 | 3 | Highly trimmed Illumina flowcell, for testing purposes. The (partial) reads from the `.bcls` come from an 4 | Illumina X10 test quality run at the Wolfson Wohl Cancer Research Centre (mainly PhiX and NA12878). 5 | 6 | bcl2fastq should be run with all `ignore` flags activated for a successful conversion: 7 | 8 | ``` 9 | bcl2fastq --ignore-missing-bcls --ignore-missing-filter --ignore-missing-positions --ignore-missing-controls 10 | ``` 11 | 12 | Prior art (from older sequencing machines) can be found in the Picard `testdata`, although this flowcell 13 | contains more metadata that could be useful: 14 | 15 | https://github.com/broadinstitute/picard/tree/master/testdata/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001 16 | 17 | Please contact Roman Valls Guimera (`brainstorm at nopcode org`) for further information. 18 | -------------------------------------------------------------------------------- /flowcell/RTAComplete.txt: -------------------------------------------------------------------------------- 1 | RTA 2.7.1 completed on 10/8/2015 1:20:47 AM 2 | -------------------------------------------------------------------------------- /flowcell/RTAConfiguration.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 25 5 | 24 6 | DataManagerAllOnDisk 7 | InterOpManagerBase 8 | ThumbnailManager 9 | S:\Illumina\HiSeqTemp 10 | 11 | WorkProviderMultiImageService 12 | 13 | .* 14 | 1_1102|1_2202|1_1215|1_2115|4_1106|4_2206|4_1219|4_2119|8_1110|8_2210|8_1223|8_2123 15 | 16 | 3 17 | 5 18 | false 19 | 12.5 20 | .* 21 | false 22 | 2 23 | 200 24 | 256 25 | http://localhost:8080/ 26 | 8082 27 | http://localhost:8090/ 28 | 4320 29 | 30 | 31 | 200 32 | 5242880 33 | true 34 | false 35 | 36 | 37 | 5 38 | 0.7 39 | 1 40 | 5 41 | 6400000 42 | 0.2 43 | 1.5 44 | LaplacianCross 45 | PatternedHexagon 46 | FullImage 47 | 48 | 0 49 | -1 50 | 0 51 | -1 52 | 5 53 | -1 54 | 0 55 | -1 56 | 0 57 | 58 | 64 59 | 64 60 | -1 61 | -1 62 | 256 63 | 256 64 | 3 65 | 66 | 67 | 3 68 | false 69 | 70 | 71 | false 72 | 1.5 73 | 1000 74 | true 75 | true 76 | OnePointFivePixel 77 | 78 | 0 79 | -1.5 80 | 0 81 | -1 82 | 6 83 | -1 84 | 0 85 | -1.5 86 | 0 87 | 88 | 1085 89 | 1810 90 | 64 91 | 64 92 | 93 | Fiducial 94 | Horizontal 95 | 1 96 | XFieldOfView 97 | 507 98 | 2063 99 | 2.03 100 | HiSeqX.tif 101 | 102 | 1.457467E-09 103 | -3.208194E-07 104 | -2.450433E-05 105 | 1.379342E-09 106 | -4.036319E-07 107 | 3.143317E-05 108 | 1.551217E-09 109 | -3.864444E-07 110 | -1.575433E-05 111 | 1.551217E-09 112 | -3.255069E-07 113 | 6.433172E-06 114 | 115 | 116 | -1.8125E-07 117 | -1.65625E-07 118 | 0 119 | -6.25E-08 120 | -2.015625E-07 121 | 0 122 | 6.375E-07 123 | 1.1875E-07 124 | 0 125 | 7.875E-07 126 | -9.375E-08 127 | 0 128 | 129 | 0 130 | 4294967295 131 | 256 132 | 200 133 | 512 134 | 135 | 136 | true 137 | 3 138 | 10 139 | 140 | 141 | BasecallerFourChannel 142 | 1 143 | GTCA 144 | 145 | true 146 | 1.19025E-07 147 | 0.6 148 | false 149 | false 150 | HiSeqX_qtable_binned.2.10.1.txt 151 | false 152 | false 153 | -1 154 | 255 155 | 156 | 157 | SequenceAlignerBits 158 | false 159 | 160 | 161 | Console 162 | FileByTile 163 | 164 | -------------------------------------------------------------------------------- /flowcell/RTARead1Complete.txt: -------------------------------------------------------------------------------- 1 | Read 1 complete 10/6/2015 10:22:34 PM -------------------------------------------------------------------------------- /flowcell/RTARead2Complete.txt: -------------------------------------------------------------------------------- 1 | Read 2 complete 10/8/2015 1:20:47 AM -------------------------------------------------------------------------------- /flowcell/SampleSheet.csv: -------------------------------------------------------------------------------- 1 | [Header],,,,,,,, 2 | IEMFileVersion,4,,,,,,, 3 | Investigator Name,,,,,,,, 4 | Experiment Name,,,,,,,, 5 | Date,10/15/2015,,,,,,, 6 | Workflow,GenerateFASTQ,,,,,,, 7 | Application,HiSeq FASTQ Only,,,,,,, 8 | Assay,TruSeq LT,,,,,,, 9 | Description,,,,,,,, 10 | Chemistry,Default,,,,,,, 11 | ,,,,,,,, 12 | [Reads],,,,,,,, 13 | 151,,,,,,,, 14 | 151,,,,,,,, 15 | ,,,,,,,, 16 | [Settings],,,,,,,, 17 | Adapter,AGATCGGAAGAGCACACGTCTGAACTCCAGTCA,,,,,,, 18 | AdapterRead2,AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT,,,,,,, 19 | ,,,,,,,, 20 | [Data],,,,,,,, 21 | Lane,Sample_ID,Sample_Name,Sample_Plate,Sample_Well,I7_Index_ID,index,Sample_Project,Description 22 | 1,PhiX,PhiX,PhiX,,,,Test,PhiX 23 | 2,PhiX,PhiX,PhiX,,,,Test,PhiX 24 | 3,NA12878_100pM,NA12878_100pM,NA12878_100pM,,A016,CCGTCC,Test,NA12878_100pM 25 | 4,NA12878_200pM,NA12878_200pM,NA12878_200pM,,A016,CCGTCC,Test,NA12878_200pM 26 | 5,NA12878_300pM,NA12878_300pM,NA12878_300pM,,A016,CCGTCC,Test,NA12878_300pM 27 | 6,NA12878_400pM,NA12878_400pM,NA12878_400pM,,A016,CCGTCC,Test,NA12878_400pM 28 | 7,PhiX,PhiX,PhiX,,,,Test,PhiX 29 | 8,PhiX,PhiX,PhiX,,,,Test,PhiX 30 | -------------------------------------------------------------------------------- /flowcell/SequencingComplete.txt: -------------------------------------------------------------------------------- 1 | Sequencing for flowcell B completed on 10/8/2015 1:33:35 AM 2 | -------------------------------------------------------------------------------- /flowcell/runParameters.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | false 5 | 2 6 | H10 7 | -999 8 | B 9 | NOINDEX 10 | 151 11 | 0 12 | 0 13 | 151 14 | X:\hiseqx_data 15 | Save All Thumbnails 16 | HiSeq X 17 | true 18 | HiSeq X SBS 19 | HiSeq X PE 20 | 21 | None 22 | false 23 | HiSeq Control Software 24 | 3.3.39 25 | 151005_ST-00295_0022_BHH5VTCCXX 26 | 151005 27 | 28 | 29 | 14987989 30 | O:\Illumina\HiSeqTemp 31 | false 32 | true 33 | false 34 | 35 | ST-00295 36 | 22 37 | HISEQXTEN 38 | 10.37.13 39 | 3.0.0 40 | 2.7.1 41 | 2.5.2.28 42 | Illumina,Bruno Fluidics Controller,0,v2.0420 43 | 2.21-C00-R04 44 | 7.5.180.4395 45 | 2.12.0.0 46 | 47 | HH5VTCCXX 48 | H7WJCCCXX 49 | MG 50 | 51 |
52 |
53 |
54 |
55 |
56 |
57 |
58 |
59 | 60 | DynamicITF 61 | BothLaneSurfaces 62 | AutoSwath 63 | true 64 | true 65 | true 66 | true 67 | false 68 | 69 | 3 70 | 7 71 | 0 72 | 250 73 | 250 74 | 0 75 | 200 76 | 21 77 | 1 78 | 100 79 | 50 80 | 20 81 | 65535 82 | 50 83 | 4 84 | 85 | 3200 86 | 7241 87 | 3200 88 | 174420 89 | 60.175 90 | 24 91 | 2 92 | false 93 | 94 | 95 | 96 | 97 | 98 | 99 | 100 | RGT6194615 101 | false 102 | 310 103 | false 104 | false 105 | true 106 | 107 | 108 | 109 | 110 | RGT5713373 111 | 112 | 113 | 114 | 115 | 116 | 117 | O:\Illumina\HiSeqTemp\151005_ST-00295_0022_BHH5VTCCXX 118 | 3.2.4 119 | false 120 | false 121 | 122 | false 123 | 124 | 1 125 | 126 | -------------------------------------------------------------------------------- /genomes/ERCC/ERCC92/bowtie2/ERCC92.1.bt2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/roryk/tiny-test-data/4dc37f0aaf5b2f3eec260a91689effa4197bd2a3/genomes/ERCC/ERCC92/bowtie2/ERCC92.1.bt2 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https://raw.githubusercontent.com/roryk/tiny-test-data/4dc37f0aaf5b2f3eec260a91689effa4197bd2a3/genomes/ERCC/ERCC92/bowtie2/ERCC92.4.bt2 -------------------------------------------------------------------------------- /genomes/ERCC/ERCC92/bowtie2/ERCC92.rev.1.bt2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/roryk/tiny-test-data/4dc37f0aaf5b2f3eec260a91689effa4197bd2a3/genomes/ERCC/ERCC92/bowtie2/ERCC92.rev.1.bt2 -------------------------------------------------------------------------------- /genomes/ERCC/ERCC92/bowtie2/ERCC92.rev.2.bt2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/roryk/tiny-test-data/4dc37f0aaf5b2f3eec260a91689effa4197bd2a3/genomes/ERCC/ERCC92/bowtie2/ERCC92.rev.2.bt2 -------------------------------------------------------------------------------- /genomes/ERCC/ERCC92/meta/ERCC_Controls_Analysis.txt: -------------------------------------------------------------------------------- 1 | Re-sort ID ERCC ID subgroup concentration in Mix 1 (attomoles/ul) concentration in Mix 2 (attomoles/ul) expected fold-change ratio log2(Mix 1/Mix 2) 2 | 1 ERCC-00130 A 30000 7500 4 2 3 | 2 ERCC-00004 A 7500 1875 4 2 4 | 3 ERCC-00136 A 1875 468.75 4 2 5 | 4 ERCC-00108 A 937.5 234.375 4 2 6 | 5 ERCC-00116 A 468.75 117.1875 4 2 7 | 6 ERCC-00092 A 234.375 58.59375 4 2 8 | 7 ERCC-00095 A 117.1875 29.296875 4 2 9 | 8 ERCC-00131 A 117.1875 29.296875 4 2 10 | 9 ERCC-00062 A 58.59375 14.6484375 4 2 11 | 10 ERCC-00019 A 29.296875 7.32421875 4 2 12 | 11 ERCC-00144 A 29.296875 7.32421875 4 2 13 | 12 ERCC-00170 A 14.6484375 3.66210938 4 2 14 | 13 ERCC-00154 A 7.32421875 1.83105469 4 2 15 | 14 ERCC-00085 A 7.32421875 1.83105469 4 2 16 | 15 ERCC-00028 A 3.66210938 0.91552734 4 2 17 | 16 ERCC-00033 A 1.83105469 0.45776367 4 2 18 | 17 ERCC-00134 A 1.83105469 0.45776367 4 2 19 | 18 ERCC-00147 A 0.91552734 0.22888184 4 2 20 | 19 ERCC-00097 A 0.45776367 0.11444092 4 2 21 | 20 ERCC-00156 A 0.45776367 0.11444092 4 2 22 | 21 ERCC-00123 A 0.22888184 0.05722046 4 2 23 | 22 ERCC-00017 A 0.11444092 0.02861023 4 2 24 | 23 ERCC-00083 A 0.02861023 0.00715256 4 2 25 | 24 ERCC-00096 B 15000 15000 1 0 26 | 25 ERCC-00171 B 3750 3750 1 0 27 | 26 ERCC-00009 B 937.5 937.5 1 0 28 | 27 ERCC-00042 B 468.75 468.75 1 0 29 | 28 ERCC-00060 B 234.375 234.375 1 0 30 | 29 ERCC-00035 B 117.1875 117.1875 1 0 31 | 30 ERCC-00025 B 58.59375 58.59375 1 0 32 | 31 ERCC-00051 B 58.59375 58.59375 1 0 33 | 32 ERCC-00053 B 29.296875 29.296875 1 0 34 | 33 ERCC-00148 B 14.6484375 14.6484375 1 0 35 | 34 ERCC-00126 B 14.6484375 14.6484375 1 0 36 | 35 ERCC-00034 B 7.32421875 7.32421875 1 0 37 | 36 ERCC-00150 B 3.66210938 3.66210938 1 0 38 | 37 ERCC-00067 B 3.66210938 3.66210938 1 0 39 | 38 ERCC-00031 B 1.83105469 1.83105469 1 0 40 | 39 ERCC-00109 B 0.91552734 0.91552734 1 0 41 | 40 ERCC-00073 B 0.91552734 0.91552734 1 0 42 | 41 ERCC-00158 B 0.45776367 0.45776367 1 0 43 | 42 ERCC-00104 B 0.22888184 0.22888184 1 0 44 | 43 ERCC-00142 B 0.22888184 0.22888184 1 0 45 | 44 ERCC-00138 B 0.11444092 0.11444092 1 0 46 | 45 ERCC-00117 B 0.05722046 0.05722046 1 0 47 | 46 ERCC-00075 B 0.01430512 0.01430512 1 0 48 | 47 ERCC-00074 C 15000 22500 0.67 -0.58 49 | 48 ERCC-00113 C 3750 5625 0.67 -0.58 50 | 49 ERCC-00145 C 937.5 1406.25 0.67 -0.58 51 | 50 ERCC-00111 C 468.75 703.125 0.67 -0.58 52 | 51 ERCC-00076 C 234.375 351.5625 0.67 -0.58 53 | 52 ERCC-00044 C 117.1875 175.78125 0.67 -0.58 54 | 53 ERCC-00162 C 58.59375 87.890625 0.67 -0.58 55 | 54 ERCC-00071 C 58.59375 87.890625 0.67 -0.58 56 | 55 ERCC-00084 C 29.296875 43.9453125 0.67 -0.58 57 | 56 ERCC-00099 C 14.6484375 21.9726563 0.67 -0.58 58 | 57 ERCC-00054 C 14.6484375 21.9726563 0.67 -0.58 59 | 58 ERCC-00157 C 7.32421875 10.9863281 0.67 -0.58 60 | 59 ERCC-00143 C 3.66210938 5.49316406 0.67 -0.58 61 | 60 ERCC-00039 C 3.66210938 5.49316406 0.67 -0.58 62 | 61 ERCC-00058 C 1.83105469 2.74658203 0.67 -0.58 63 | 62 ERCC-00120 C 0.91552734 1.37329102 0.67 -0.58 64 | 63 ERCC-00040 C 0.91552734 1.37329102 0.67 -0.58 65 | 64 ERCC-00164 C 0.45776367 0.68664551 0.67 -0.58 66 | 65 ERCC-00024 C 0.22888184 0.34332275 0.67 -0.58 67 | 66 ERCC-00016 C 0.22888184 0.34332275 0.67 -0.58 68 | 67 ERCC-00012 C 0.11444092 0.17166138 0.67 -0.58 69 | 68 ERCC-00098 C 0.05722046 0.08583069 0.67 -0.58 70 | 69 ERCC-00057 C 0.01430512 0.02145767 0.67 -0.58 71 | 70 ERCC-00002 D 15000 30000 0.5 -1 72 | 71 ERCC-00046 D 3750 7500 0.5 -1 73 | 72 ERCC-00003 D 937.5 1875 0.5 -1 74 | 73 ERCC-00043 D 468.75 937.5 0.5 -1 75 | 74 ERCC-00022 D 234.375 468.75 0.5 -1 76 | 75 ERCC-00112 D 117.1875 234.375 0.5 -1 77 | 76 ERCC-00165 D 58.59375 117.1875 0.5 -1 78 | 77 ERCC-00079 D 58.59375 117.1875 0.5 -1 79 | 78 ERCC-00078 D 29.296875 58.59375 0.5 -1 80 | 79 ERCC-00163 D 14.6484375 29.296875 0.5 -1 81 | 80 ERCC-00059 D 14.6484375 29.296875 0.5 -1 82 | 81 ERCC-00160 D 7.32421875 14.6484375 0.5 -1 83 | 82 ERCC-00014 D 3.66210938 7.32421875 0.5 -1 84 | 83 ERCC-00077 D 3.66210938 7.32421875 0.5 -1 85 | 84 ERCC-00069 D 1.83105469 3.66210938 0.5 -1 86 | 85 ERCC-00137 D 0.91552734 1.83105469 0.5 -1 87 | 86 ERCC-00013 D 0.91552734 1.83105469 0.5 -1 88 | 87 ERCC-00168 D 0.45776367 0.91552734 0.5 -1 89 | 88 ERCC-00041 D 0.22888184 0.45776367 0.5 -1 90 | 89 ERCC-00081 D 0.22888184 0.45776367 0.5 -1 91 | 90 ERCC-00086 D 0.11444092 0.22888184 0.5 -1 92 | 91 ERCC-00061 D 0.05722046 0.11444092 0.5 -1 93 | 92 ERCC-00048 D 0.01430512 0.02861023 0.5 -1 94 | -------------------------------------------------------------------------------- /genomes/ERCC/ERCC92/rnaseq/ref-transcripts.gtf: -------------------------------------------------------------------------------- 1 | ERCC-00002 ERCC exon 1 1061 0.000000 + . gene_id "ERCC-00002"; transcript_id "DQ459430"; 2 | ERCC-00003 ERCC exon 1 1023 0.000000 + . gene_id "ERCC-00003"; transcript_id "DQ516784"; 3 | ERCC-00004 ERCC exon 1 523 0.000000 + . gene_id "ERCC-00004"; transcript_id "DQ516752"; 4 | ERCC-00009 ERCC exon 1 984 0.000000 + . gene_id "ERCC-00009"; transcript_id "DQ668364"; 5 | ERCC-00012 ERCC exon 1 994 0.000000 + . gene_id "ERCC-00012"; transcript_id "DQ883670"; 6 | ERCC-00013 ERCC exon 1 808 0.000000 + . gene_id "ERCC-00013"; transcript_id "EF011062"; 7 | ERCC-00014 ERCC exon 1 1957 0.000000 + . gene_id "ERCC-00014"; transcript_id "DQ875385"; 8 | ERCC-00016 ERCC exon 1 844 0.000000 + . gene_id "ERCC-00016"; transcript_id "DQ883664"; 9 | ERCC-00017 ERCC exon 1 1136 0.000000 + . gene_id "ERCC-00017"; transcript_id "DQ459420"; 10 | ERCC-00019 ERCC exon 1 644 0.000000 + . gene_id "ERCC-00019"; transcript_id "DQ883651"; 11 | ERCC-00022 ERCC exon 1 751 0.000000 + . gene_id "ERCC-00022"; transcript_id "DQ855004"; 12 | ERCC-00024 ERCC exon 1 536 0.000000 + . gene_id "ERCC-00024"; transcript_id "DQ854993"; 13 | ERCC-00025 ERCC exon 1 1994 0.000000 + . gene_id "ERCC-00025"; transcript_id "DQ883689"; 14 | ERCC-00028 ERCC exon 1 1130 0.000000 + . gene_id "ERCC-00028"; transcript_id "DQ459419"; 15 | ERCC-00031 ERCC exon 1 1138 0.000000 + . gene_id "ERCC-00031"; transcript_id "DQ459431"; 16 | ERCC-00033 ERCC exon 1 2022 0.000000 + . gene_id "ERCC-00033"; transcript_id "DQ516796"; 17 | ERCC-00034 ERCC exon 1 1019 0.000000 + . gene_id "ERCC-00034"; transcript_id "DQ855001"; 18 | ERCC-00035 ERCC exon 1 1130 0.000000 + . gene_id "ERCC-00035"; transcript_id "DQ459413"; 19 | ERCC-00039 ERCC exon 1 740 0.000000 + . gene_id "ERCC-00039"; transcript_id "DQ883656"; 20 | ERCC-00040 ERCC exon 1 744 0.000000 + . gene_id "ERCC-00040"; transcript_id "DQ883661"; 21 | ERCC-00041 ERCC exon 1 1122 0.000000 + . gene_id "ERCC-00041"; transcript_id "EF011069"; 22 | ERCC-00042 ERCC exon 1 1023 0.000000 + . gene_id "ERCC-00042"; transcript_id "DQ516783"; 23 | ERCC-00043 ERCC exon 1 1023 0.000000 + . gene_id "ERCC-00043"; transcript_id "DQ516787"; 24 | ERCC-00044 ERCC exon 1 1156 0.000000 + . gene_id "ERCC-00044"; transcript_id "DQ459424"; 25 | ERCC-00046 ERCC exon 1 522 0.000000 + . gene_id "ERCC-00046"; transcript_id "DQ516748"; 26 | ERCC-00048 ERCC exon 1 992 0.000000 + . gene_id "ERCC-00048"; transcript_id "DQ883671"; 27 | ERCC-00051 ERCC exon 1 274 0.000000 + . gene_id "ERCC-00051"; transcript_id "DQ516740"; 28 | ERCC-00053 ERCC exon 1 1023 0.000000 + . gene_id "ERCC-00053"; transcript_id "DQ516785"; 29 | ERCC-00054 ERCC exon 1 274 0.000000 + . gene_id "ERCC-00054"; transcript_id "DQ516731"; 30 | ERCC-00057 ERCC exon 1 1021 0.000000 + . gene_id "ERCC-00057"; transcript_id "DQ668366"; 31 | ERCC-00058 ERCC exon 1 1136 0.000000 + . gene_id "ERCC-00058"; transcript_id "DQ459418"; 32 | ERCC-00059 ERCC exon 1 525 0.000000 + . gene_id "ERCC-00059"; transcript_id "DQ668356"; 33 | ERCC-00060 ERCC exon 1 523 0.000000 + . gene_id "ERCC-00060"; transcript_id "DQ516763"; 34 | ERCC-00061 ERCC exon 1 1136 0.000000 + . gene_id "ERCC-00061"; transcript_id "DQ459426"; 35 | ERCC-00062 ERCC exon 1 1023 0.000000 + . gene_id "ERCC-00062"; transcript_id "DQ516786"; 36 | ERCC-00067 ERCC exon 1 644 0.000000 + . gene_id "ERCC-00067"; transcript_id "DQ883653"; 37 | ERCC-00069 ERCC exon 1 1137 0.000000 + . gene_id "ERCC-00069"; transcript_id "DQ459421"; 38 | ERCC-00071 ERCC exon 1 642 0.000000 + . gene_id "ERCC-00071"; transcript_id "DQ883654"; 39 | ERCC-00073 ERCC exon 1 603 0.000000 + . gene_id "ERCC-00073"; transcript_id "DQ668358"; 40 | ERCC-00074 ERCC exon 1 522 0.000000 + . gene_id "ERCC-00074"; transcript_id "DQ516754"; 41 | ERCC-00075 ERCC exon 1 1023 0.000000 + . gene_id "ERCC-00075"; transcript_id "DQ516778"; 42 | ERCC-00076 ERCC exon 1 642 0.000000 + . gene_id "ERCC-00076"; transcript_id "DQ883650"; 43 | ERCC-00077 ERCC exon 1 273 0.000000 + . gene_id "ERCC-00077"; transcript_id "DQ516742"; 44 | ERCC-00078 ERCC exon 1 993 0.000000 + . gene_id "ERCC-00078"; transcript_id "DQ883673"; 45 | ERCC-00079 ERCC exon 1 644 0.000000 + . gene_id "ERCC-00079"; transcript_id "DQ883652"; 46 | ERCC-00081 ERCC exon 1 534 0.000000 + . gene_id "ERCC-00081"; transcript_id "DQ854991"; 47 | ERCC-00083 ERCC exon 1 1022 0.000000 + . gene_id "ERCC-00083"; transcript_id "DQ516780"; 48 | ERCC-00084 ERCC exon 1 994 0.000000 + . gene_id "ERCC-00084"; transcript_id "DQ883682"; 49 | ERCC-00085 ERCC exon 1 844 0.000000 + . gene_id "ERCC-00085"; transcript_id "DQ883669"; 50 | ERCC-00086 ERCC exon 1 1020 0.000000 + . gene_id "ERCC-00086"; transcript_id "DQ516791"; 51 | ERCC-00092 ERCC exon 1 1124 0.000000 + . gene_id "ERCC-00092"; transcript_id "DQ459425"; 52 | ERCC-00095 ERCC exon 1 521 0.000000 + . gene_id "ERCC-00095"; transcript_id "DQ516759"; 53 | ERCC-00096 ERCC exon 1 1107 0.000000 + . gene_id "ERCC-00096"; transcript_id "DQ459429"; 54 | ERCC-00097 ERCC exon 1 523 0.000000 + . gene_id "ERCC-00097"; transcript_id "DQ516758"; 55 | ERCC-00098 ERCC exon 1 1143 0.000000 + . gene_id "ERCC-00098"; transcript_id "DQ459415"; 56 | ERCC-00099 ERCC exon 1 1350 0.000000 + . gene_id "ERCC-00099"; transcript_id "DQ875387"; 57 | ERCC-00104 ERCC exon 1 2022 0.000000 + . gene_id "ERCC-00104"; transcript_id "DQ516815"; 58 | ERCC-00108 ERCC exon 1 1022 0.000000 + . gene_id "ERCC-00108"; transcript_id "DQ668365"; 59 | ERCC-00109 ERCC exon 1 536 0.000000 + . gene_id "ERCC-00109"; transcript_id "DQ854998"; 60 | ERCC-00111 ERCC exon 1 994 0.000000 + . gene_id "ERCC-00111"; transcript_id "DQ883685"; 61 | ERCC-00112 ERCC exon 1 1136 0.000000 + . gene_id "ERCC-00112"; transcript_id "DQ459422"; 62 | ERCC-00113 ERCC exon 1 840 0.000000 + . gene_id "ERCC-00113"; transcript_id "DQ883663"; 63 | ERCC-00116 ERCC exon 1 1991 0.000000 + . gene_id "ERCC-00116"; transcript_id "DQ668367"; 64 | ERCC-00117 ERCC exon 1 1136 0.000000 + . gene_id "ERCC-00117"; transcript_id "DQ459412"; 65 | ERCC-00120 ERCC exon 1 536 0.000000 + . gene_id "ERCC-00120"; transcript_id "DQ854992"; 66 | ERCC-00123 ERCC exon 1 1022 0.000000 + . gene_id "ERCC-00123"; transcript_id "DQ516782"; 67 | ERCC-00126 ERCC exon 1 1118 0.000000 + . gene_id "ERCC-00126"; transcript_id "DQ459427"; 68 | ERCC-00130 ERCC exon 1 1059 0.000000 + . gene_id "ERCC-00130"; transcript_id "EF011072"; 69 | ERCC-00131 ERCC exon 1 771 0.000000 + . gene_id "ERCC-00131"; transcript_id "DQ855003"; 70 | ERCC-00134 ERCC exon 1 274 0.000000 + . gene_id "ERCC-00134"; transcript_id "DQ516739"; 71 | ERCC-00136 ERCC exon 1 1033 0.000000 + . gene_id "ERCC-00136"; transcript_id "EF011063"; 72 | ERCC-00137 ERCC exon 1 537 0.000000 + . gene_id "ERCC-00137"; transcript_id "DQ855000"; 73 | ERCC-00138 ERCC exon 1 1024 0.000000 + . gene_id "ERCC-00138"; transcript_id "DQ516777"; 74 | ERCC-00142 ERCC exon 1 493 0.000000 + . gene_id "ERCC-00142"; transcript_id "DQ883646"; 75 | ERCC-00143 ERCC exon 1 784 0.000000 + . gene_id "ERCC-00143"; transcript_id "DQ668362"; 76 | ERCC-00144 ERCC exon 1 538 0.000000 + . gene_id "ERCC-00144"; transcript_id "DQ854995"; 77 | ERCC-00145 ERCC exon 1 1042 0.000000 + . gene_id "ERCC-00145"; transcript_id "DQ875386"; 78 | ERCC-00147 ERCC exon 1 1023 0.000000 + . gene_id "ERCC-00147"; transcript_id "DQ516790"; 79 | ERCC-00148 ERCC exon 1 494 0.000000 + . gene_id "ERCC-00148"; transcript_id "DQ883642"; 80 | ERCC-00150 ERCC exon 1 743 0.000000 + . gene_id "ERCC-00150"; transcript_id "DQ883659"; 81 | ERCC-00154 ERCC exon 1 537 0.000000 + . gene_id "ERCC-00154"; transcript_id "DQ854997"; 82 | ERCC-00156 ERCC exon 1 494 0.000000 + . gene_id "ERCC-00156"; transcript_id "DQ883643"; 83 | ERCC-00157 ERCC exon 1 1019 0.000000 + . gene_id "ERCC-00157"; transcript_id "DQ839618"; 84 | ERCC-00158 ERCC exon 1 1027 0.000000 + . gene_id "ERCC-00158"; transcript_id "DQ516795"; 85 | ERCC-00160 ERCC exon 1 743 0.000000 + . gene_id "ERCC-00160"; transcript_id "DQ883658"; 86 | ERCC-00162 ERCC exon 1 523 0.000000 + . gene_id "ERCC-00162"; transcript_id "DQ516750"; 87 | ERCC-00163 ERCC exon 1 543 0.000000 + . gene_id "ERCC-00163"; transcript_id "DQ668359"; 88 | ERCC-00164 ERCC exon 1 1022 0.000000 + . gene_id "ERCC-00164"; transcript_id "DQ516779"; 89 | ERCC-00165 ERCC exon 1 872 0.000000 + . gene_id "ERCC-00165"; transcript_id "DQ668363"; 90 | ERCC-00168 ERCC exon 1 1024 0.000000 + . gene_id "ERCC-00168"; transcript_id "DQ516776"; 91 | ERCC-00170 ERCC exon 1 1023 0.000000 + . gene_id "ERCC-00170"; transcript_id "DQ516773"; 92 | ERCC-00171 ERCC exon 1 505 0.000000 + . gene_id "ERCC-00171"; transcript_id "DQ854994"; 93 | -------------------------------------------------------------------------------- /genomes/ERCC/ERCC92/rnaseq/tophat/ERCC92.1.bt2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/roryk/tiny-test-data/4dc37f0aaf5b2f3eec260a91689effa4197bd2a3/genomes/ERCC/ERCC92/rnaseq/tophat/ERCC92.1.bt2 -------------------------------------------------------------------------------- /genomes/ERCC/ERCC92/rnaseq/tophat/ERCC92.2.bt2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/roryk/tiny-test-data/4dc37f0aaf5b2f3eec260a91689effa4197bd2a3/genomes/ERCC/ERCC92/rnaseq/tophat/ERCC92.2.bt2 -------------------------------------------------------------------------------- /genomes/ERCC/ERCC92/rnaseq/tophat/ERCC92.3.bt2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/roryk/tiny-test-data/4dc37f0aaf5b2f3eec260a91689effa4197bd2a3/genomes/ERCC/ERCC92/rnaseq/tophat/ERCC92.3.bt2 -------------------------------------------------------------------------------- /genomes/ERCC/ERCC92/rnaseq/tophat/ERCC92.4.bt2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/roryk/tiny-test-data/4dc37f0aaf5b2f3eec260a91689effa4197bd2a3/genomes/ERCC/ERCC92/rnaseq/tophat/ERCC92.4.bt2 -------------------------------------------------------------------------------- /genomes/ERCC/ERCC92/rnaseq/tophat/ERCC92.fa.tlst: -------------------------------------------------------------------------------- 1 | 0 DQ459430 ERCC-00002+ 1-1061 2 | 1 DQ516784 ERCC-00003+ 1-1023 3 | 2 DQ516752 ERCC-00004+ 1-523 4 | 3 DQ668364 ERCC-00009+ 1-984 5 | 4 DQ883670 ERCC-00012+ 1-994 6 | 5 EF011062 ERCC-00013+ 1-808 7 | 6 DQ875385 ERCC-00014+ 1-1957 8 | 7 DQ883664 ERCC-00016+ 1-844 9 | 8 DQ459420 ERCC-00017+ 1-1136 10 | 9 DQ883651 ERCC-00019+ 1-644 11 | 10 DQ855004 ERCC-00022+ 1-751 12 | 11 DQ854993 ERCC-00024+ 1-536 13 | 12 DQ883689 ERCC-00025+ 1-1994 14 | 13 DQ459419 ERCC-00028+ 1-1130 15 | 14 DQ459431 ERCC-00031+ 1-1138 16 | 15 DQ516796 ERCC-00033+ 1-2022 17 | 16 DQ855001 ERCC-00034+ 1-1019 18 | 17 DQ459413 ERCC-00035+ 1-1130 19 | 18 DQ883656 ERCC-00039+ 1-740 20 | 19 DQ883661 ERCC-00040+ 1-744 21 | 20 EF011069 ERCC-00041+ 1-1122 22 | 21 DQ516783 ERCC-00042+ 1-1023 23 | 22 DQ516787 ERCC-00043+ 1-1023 24 | 23 DQ459424 ERCC-00044+ 1-1156 25 | 24 DQ516748 ERCC-00046+ 1-522 26 | 25 DQ883671 ERCC-00048+ 1-992 27 | 26 DQ516740 ERCC-00051+ 1-274 28 | 27 DQ516785 ERCC-00053+ 1-1023 29 | 28 DQ516731 ERCC-00054+ 1-274 30 | 29 DQ668366 ERCC-00057+ 1-1021 31 | 30 DQ459418 ERCC-00058+ 1-1136 32 | 31 DQ668356 ERCC-00059+ 1-525 33 | 32 DQ516763 ERCC-00060+ 1-523 34 | 33 DQ459426 ERCC-00061+ 1-1136 35 | 34 DQ516786 ERCC-00062+ 1-1023 36 | 35 DQ883653 ERCC-00067+ 1-644 37 | 36 DQ459421 ERCC-00069+ 1-1137 38 | 37 DQ883654 ERCC-00071+ 1-642 39 | 38 DQ668358 ERCC-00073+ 1-603 40 | 39 DQ516754 ERCC-00074+ 1-522 41 | 40 DQ516778 ERCC-00075+ 1-1023 42 | 41 DQ883650 ERCC-00076+ 1-642 43 | 42 DQ516742 ERCC-00077+ 1-273 44 | 43 DQ883673 ERCC-00078+ 1-993 45 | 44 DQ883652 ERCC-00079+ 1-644 46 | 45 DQ854991 ERCC-00081+ 1-534 47 | 46 DQ516780 ERCC-00083+ 1-1022 48 | 47 DQ883682 ERCC-00084+ 1-994 49 | 48 DQ883669 ERCC-00085+ 1-844 50 | 49 DQ516791 ERCC-00086+ 1-1020 51 | 50 DQ459425 ERCC-00092+ 1-1124 52 | 51 DQ516759 ERCC-00095+ 1-521 53 | 52 DQ459429 ERCC-00096+ 1-1107 54 | 53 DQ516758 ERCC-00097+ 1-523 55 | 54 DQ459415 ERCC-00098+ 1-1143 56 | 55 DQ875387 ERCC-00099+ 1-1350 57 | 56 DQ516815 ERCC-00104+ 1-2022 58 | 57 DQ668365 ERCC-00108+ 1-1022 59 | 58 DQ854998 ERCC-00109+ 1-536 60 | 59 DQ883685 ERCC-00111+ 1-994 61 | 60 DQ459422 ERCC-00112+ 1-1136 62 | 61 DQ883663 ERCC-00113+ 1-840 63 | 62 DQ668367 ERCC-00116+ 1-1991 64 | 63 DQ459412 ERCC-00117+ 1-1136 65 | 64 DQ854992 ERCC-00120+ 1-536 66 | 65 DQ516782 ERCC-00123+ 1-1022 67 | 66 DQ459427 ERCC-00126+ 1-1118 68 | 67 EF011072 ERCC-00130+ 1-1059 69 | 68 DQ855003 ERCC-00131+ 1-771 70 | 69 DQ516739 ERCC-00134+ 1-274 71 | 70 EF011063 ERCC-00136+ 1-1033 72 | 71 DQ855000 ERCC-00137+ 1-537 73 | 72 DQ516777 ERCC-00138+ 1-1024 74 | 73 DQ883646 ERCC-00142+ 1-493 75 | 74 DQ668362 ERCC-00143+ 1-784 76 | 75 DQ854995 ERCC-00144+ 1-538 77 | 76 DQ875386 ERCC-00145+ 1-1042 78 | 77 DQ516790 ERCC-00147+ 1-1023 79 | 78 DQ883642 ERCC-00148+ 1-494 80 | 79 DQ883659 ERCC-00150+ 1-743 81 | 80 DQ854997 ERCC-00154+ 1-537 82 | 81 DQ883643 ERCC-00156+ 1-494 83 | 82 DQ839618 ERCC-00157+ 1-1019 84 | 83 DQ516795 ERCC-00158+ 1-1027 85 | 84 DQ883658 ERCC-00160+ 1-743 86 | 85 DQ516750 ERCC-00162+ 1-523 87 | 86 DQ668359 ERCC-00163+ 1-543 88 | 87 DQ516779 ERCC-00164+ 1-1022 89 | 88 DQ668363 ERCC-00165+ 1-872 90 | 89 DQ516776 ERCC-00168+ 1-1024 91 | 90 DQ516773 ERCC-00170+ 1-1023 92 | 91 DQ854994 ERCC-00171+ 1-505 93 | -------------------------------------------------------------------------------- /genomes/ERCC/ERCC92/rnaseq/tophat/ERCC92.gff: -------------------------------------------------------------------------------- 1 | ERCC-00002 ERCC exon 1 1061 0.000000 + . gene_id "ERCC-00002"; transcript_id "DQ459430"; 2 | ERCC-00003 ERCC exon 1 1023 0.000000 + . gene_id "ERCC-00003"; transcript_id "DQ516784"; 3 | ERCC-00004 ERCC exon 1 523 0.000000 + . gene_id "ERCC-00004"; transcript_id "DQ516752"; 4 | ERCC-00009 ERCC exon 1 984 0.000000 + . gene_id "ERCC-00009"; transcript_id "DQ668364"; 5 | ERCC-00012 ERCC exon 1 994 0.000000 + . gene_id "ERCC-00012"; transcript_id "DQ883670"; 6 | ERCC-00013 ERCC exon 1 808 0.000000 + . gene_id "ERCC-00013"; transcript_id "EF011062"; 7 | ERCC-00014 ERCC exon 1 1957 0.000000 + . gene_id "ERCC-00014"; transcript_id "DQ875385"; 8 | ERCC-00016 ERCC exon 1 844 0.000000 + . gene_id "ERCC-00016"; transcript_id "DQ883664"; 9 | ERCC-00017 ERCC exon 1 1136 0.000000 + . gene_id "ERCC-00017"; transcript_id "DQ459420"; 10 | ERCC-00019 ERCC exon 1 644 0.000000 + . gene_id "ERCC-00019"; transcript_id "DQ883651"; 11 | ERCC-00022 ERCC exon 1 751 0.000000 + . gene_id "ERCC-00022"; transcript_id "DQ855004"; 12 | ERCC-00024 ERCC exon 1 536 0.000000 + . gene_id "ERCC-00024"; transcript_id "DQ854993"; 13 | ERCC-00025 ERCC exon 1 1994 0.000000 + . gene_id "ERCC-00025"; transcript_id "DQ883689"; 14 | ERCC-00028 ERCC exon 1 1130 0.000000 + . gene_id "ERCC-00028"; transcript_id "DQ459419"; 15 | ERCC-00031 ERCC exon 1 1138 0.000000 + . gene_id "ERCC-00031"; transcript_id "DQ459431"; 16 | ERCC-00033 ERCC exon 1 2022 0.000000 + . gene_id "ERCC-00033"; transcript_id "DQ516796"; 17 | ERCC-00034 ERCC exon 1 1019 0.000000 + . gene_id "ERCC-00034"; transcript_id "DQ855001"; 18 | ERCC-00035 ERCC exon 1 1130 0.000000 + . gene_id "ERCC-00035"; transcript_id "DQ459413"; 19 | ERCC-00039 ERCC exon 1 740 0.000000 + . gene_id "ERCC-00039"; transcript_id "DQ883656"; 20 | ERCC-00040 ERCC exon 1 744 0.000000 + . gene_id "ERCC-00040"; transcript_id "DQ883661"; 21 | ERCC-00041 ERCC exon 1 1122 0.000000 + . gene_id "ERCC-00041"; transcript_id "EF011069"; 22 | ERCC-00042 ERCC exon 1 1023 0.000000 + . gene_id "ERCC-00042"; transcript_id "DQ516783"; 23 | ERCC-00043 ERCC exon 1 1023 0.000000 + . gene_id "ERCC-00043"; transcript_id "DQ516787"; 24 | ERCC-00044 ERCC exon 1 1156 0.000000 + . gene_id "ERCC-00044"; transcript_id "DQ459424"; 25 | ERCC-00046 ERCC exon 1 522 0.000000 + . gene_id "ERCC-00046"; transcript_id "DQ516748"; 26 | ERCC-00048 ERCC exon 1 992 0.000000 + . gene_id "ERCC-00048"; transcript_id "DQ883671"; 27 | ERCC-00051 ERCC exon 1 274 0.000000 + . gene_id "ERCC-00051"; transcript_id "DQ516740"; 28 | ERCC-00053 ERCC exon 1 1023 0.000000 + . gene_id "ERCC-00053"; transcript_id "DQ516785"; 29 | ERCC-00054 ERCC exon 1 274 0.000000 + . gene_id "ERCC-00054"; transcript_id "DQ516731"; 30 | ERCC-00057 ERCC exon 1 1021 0.000000 + . gene_id "ERCC-00057"; transcript_id "DQ668366"; 31 | ERCC-00058 ERCC exon 1 1136 0.000000 + . gene_id "ERCC-00058"; transcript_id "DQ459418"; 32 | ERCC-00059 ERCC exon 1 525 0.000000 + . gene_id "ERCC-00059"; transcript_id "DQ668356"; 33 | ERCC-00060 ERCC exon 1 523 0.000000 + . gene_id "ERCC-00060"; transcript_id "DQ516763"; 34 | ERCC-00061 ERCC exon 1 1136 0.000000 + . gene_id "ERCC-00061"; transcript_id "DQ459426"; 35 | ERCC-00062 ERCC exon 1 1023 0.000000 + . gene_id "ERCC-00062"; transcript_id "DQ516786"; 36 | ERCC-00067 ERCC exon 1 644 0.000000 + . gene_id "ERCC-00067"; transcript_id "DQ883653"; 37 | ERCC-00069 ERCC exon 1 1137 0.000000 + . gene_id "ERCC-00069"; transcript_id "DQ459421"; 38 | ERCC-00071 ERCC exon 1 642 0.000000 + . gene_id "ERCC-00071"; transcript_id "DQ883654"; 39 | ERCC-00073 ERCC exon 1 603 0.000000 + . gene_id "ERCC-00073"; transcript_id "DQ668358"; 40 | ERCC-00074 ERCC exon 1 522 0.000000 + . gene_id "ERCC-00074"; transcript_id "DQ516754"; 41 | ERCC-00075 ERCC exon 1 1023 0.000000 + . gene_id "ERCC-00075"; transcript_id "DQ516778"; 42 | ERCC-00076 ERCC exon 1 642 0.000000 + . gene_id "ERCC-00076"; transcript_id "DQ883650"; 43 | ERCC-00077 ERCC exon 1 273 0.000000 + . gene_id "ERCC-00077"; transcript_id "DQ516742"; 44 | ERCC-00078 ERCC exon 1 993 0.000000 + . gene_id "ERCC-00078"; transcript_id "DQ883673"; 45 | ERCC-00079 ERCC exon 1 644 0.000000 + . gene_id "ERCC-00079"; transcript_id "DQ883652"; 46 | ERCC-00081 ERCC exon 1 534 0.000000 + . gene_id "ERCC-00081"; transcript_id "DQ854991"; 47 | ERCC-00083 ERCC exon 1 1022 0.000000 + . gene_id "ERCC-00083"; transcript_id "DQ516780"; 48 | ERCC-00084 ERCC exon 1 994 0.000000 + . gene_id "ERCC-00084"; transcript_id "DQ883682"; 49 | ERCC-00085 ERCC exon 1 844 0.000000 + . gene_id "ERCC-00085"; transcript_id "DQ883669"; 50 | ERCC-00086 ERCC exon 1 1020 0.000000 + . gene_id "ERCC-00086"; transcript_id "DQ516791"; 51 | ERCC-00092 ERCC exon 1 1124 0.000000 + . gene_id "ERCC-00092"; transcript_id "DQ459425"; 52 | ERCC-00095 ERCC exon 1 521 0.000000 + . gene_id "ERCC-00095"; transcript_id "DQ516759"; 53 | ERCC-00096 ERCC exon 1 1107 0.000000 + . gene_id "ERCC-00096"; transcript_id "DQ459429"; 54 | ERCC-00097 ERCC exon 1 523 0.000000 + . gene_id "ERCC-00097"; transcript_id "DQ516758"; 55 | ERCC-00098 ERCC exon 1 1143 0.000000 + . gene_id "ERCC-00098"; transcript_id "DQ459415"; 56 | ERCC-00099 ERCC exon 1 1350 0.000000 + . gene_id "ERCC-00099"; transcript_id "DQ875387"; 57 | ERCC-00104 ERCC exon 1 2022 0.000000 + . gene_id "ERCC-00104"; transcript_id "DQ516815"; 58 | ERCC-00108 ERCC exon 1 1022 0.000000 + . gene_id "ERCC-00108"; transcript_id "DQ668365"; 59 | ERCC-00109 ERCC exon 1 536 0.000000 + . gene_id "ERCC-00109"; transcript_id "DQ854998"; 60 | ERCC-00111 ERCC exon 1 994 0.000000 + . gene_id "ERCC-00111"; transcript_id "DQ883685"; 61 | ERCC-00112 ERCC exon 1 1136 0.000000 + . gene_id "ERCC-00112"; transcript_id "DQ459422"; 62 | ERCC-00113 ERCC exon 1 840 0.000000 + . gene_id "ERCC-00113"; transcript_id "DQ883663"; 63 | ERCC-00116 ERCC exon 1 1991 0.000000 + . gene_id "ERCC-00116"; transcript_id "DQ668367"; 64 | ERCC-00117 ERCC exon 1 1136 0.000000 + . gene_id "ERCC-00117"; transcript_id "DQ459412"; 65 | ERCC-00120 ERCC exon 1 536 0.000000 + . gene_id "ERCC-00120"; transcript_id "DQ854992"; 66 | ERCC-00123 ERCC exon 1 1022 0.000000 + . gene_id "ERCC-00123"; transcript_id "DQ516782"; 67 | ERCC-00126 ERCC exon 1 1118 0.000000 + . gene_id "ERCC-00126"; transcript_id "DQ459427"; 68 | ERCC-00130 ERCC exon 1 1059 0.000000 + . gene_id "ERCC-00130"; transcript_id "EF011072"; 69 | ERCC-00131 ERCC exon 1 771 0.000000 + . gene_id "ERCC-00131"; transcript_id "DQ855003"; 70 | ERCC-00134 ERCC exon 1 274 0.000000 + . gene_id "ERCC-00134"; transcript_id "DQ516739"; 71 | ERCC-00136 ERCC exon 1 1033 0.000000 + . gene_id "ERCC-00136"; transcript_id "EF011063"; 72 | ERCC-00137 ERCC exon 1 537 0.000000 + . gene_id "ERCC-00137"; transcript_id "DQ855000"; 73 | ERCC-00138 ERCC exon 1 1024 0.000000 + . gene_id "ERCC-00138"; transcript_id "DQ516777"; 74 | ERCC-00142 ERCC exon 1 493 0.000000 + . gene_id "ERCC-00142"; transcript_id "DQ883646"; 75 | ERCC-00143 ERCC exon 1 784 0.000000 + . gene_id "ERCC-00143"; transcript_id "DQ668362"; 76 | ERCC-00144 ERCC exon 1 538 0.000000 + . gene_id "ERCC-00144"; transcript_id "DQ854995"; 77 | ERCC-00145 ERCC exon 1 1042 0.000000 + . gene_id "ERCC-00145"; transcript_id "DQ875386"; 78 | ERCC-00147 ERCC exon 1 1023 0.000000 + . gene_id "ERCC-00147"; transcript_id "DQ516790"; 79 | ERCC-00148 ERCC exon 1 494 0.000000 + . gene_id "ERCC-00148"; transcript_id "DQ883642"; 80 | ERCC-00150 ERCC exon 1 743 0.000000 + . gene_id "ERCC-00150"; transcript_id "DQ883659"; 81 | ERCC-00154 ERCC exon 1 537 0.000000 + . gene_id "ERCC-00154"; transcript_id "DQ854997"; 82 | ERCC-00156 ERCC exon 1 494 0.000000 + . gene_id "ERCC-00156"; transcript_id "DQ883643"; 83 | ERCC-00157 ERCC exon 1 1019 0.000000 + . gene_id "ERCC-00157"; transcript_id "DQ839618"; 84 | ERCC-00158 ERCC exon 1 1027 0.000000 + . gene_id "ERCC-00158"; transcript_id "DQ516795"; 85 | ERCC-00160 ERCC exon 1 743 0.000000 + . gene_id "ERCC-00160"; transcript_id "DQ883658"; 86 | ERCC-00162 ERCC exon 1 523 0.000000 + . gene_id "ERCC-00162"; transcript_id "DQ516750"; 87 | ERCC-00163 ERCC exon 1 543 0.000000 + . gene_id "ERCC-00163"; transcript_id "DQ668359"; 88 | ERCC-00164 ERCC exon 1 1022 0.000000 + . gene_id "ERCC-00164"; transcript_id "DQ516779"; 89 | ERCC-00165 ERCC exon 1 872 0.000000 + . gene_id "ERCC-00165"; transcript_id "DQ668363"; 90 | ERCC-00168 ERCC exon 1 1024 0.000000 + . gene_id "ERCC-00168"; transcript_id "DQ516776"; 91 | ERCC-00170 ERCC exon 1 1023 0.000000 + . gene_id "ERCC-00170"; transcript_id "DQ516773"; 92 | ERCC-00171 ERCC exon 1 505 0.000000 + . gene_id "ERCC-00171"; transcript_id "DQ854994"; 93 | -------------------------------------------------------------------------------- /genomes/ERCC/ERCC92/rnaseq/tophat/ERCC92.rev.1.bt2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/roryk/tiny-test-data/4dc37f0aaf5b2f3eec260a91689effa4197bd2a3/genomes/ERCC/ERCC92/rnaseq/tophat/ERCC92.rev.1.bt2 -------------------------------------------------------------------------------- /genomes/ERCC/ERCC92/rnaseq/tophat/ERCC92.rev.2.bt2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/roryk/tiny-test-data/4dc37f0aaf5b2f3eec260a91689effa4197bd2a3/genomes/ERCC/ERCC92/rnaseq/tophat/ERCC92.rev.2.bt2 -------------------------------------------------------------------------------- /genomes/ERCC/ERCC92/rnaseq/tophat/ERCC92.ver: -------------------------------------------------------------------------------- 1 | 209 8140 87066 2 | -------------------------------------------------------------------------------- /genomes/ERCC/ERCC92/seq/ERCC92-resources.yaml: -------------------------------------------------------------------------------- 1 | version: 1 2 | rnaseq: 3 | transcripts: ../rnaseq/ref-transcripts.gtf 4 | -------------------------------------------------------------------------------- /genomes/Hsapiens/hg19/bowtie2/hg19.1.bt2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/roryk/tiny-test-data/4dc37f0aaf5b2f3eec260a91689effa4197bd2a3/genomes/Hsapiens/hg19/bowtie2/hg19.1.bt2 -------------------------------------------------------------------------------- /genomes/Hsapiens/hg19/bowtie2/hg19.2.bt2: -------------------------------------------------------------------------------- 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36572 2 11 2 | 0 chrM (null) 3 | 0 16571 0 4 | 0 chr22 (null) 5 | 16571 20001 0 6 | -------------------------------------------------------------------------------- /genomes/Hsapiens/hg19/bwa/hg19.fa.bwt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/roryk/tiny-test-data/4dc37f0aaf5b2f3eec260a91689effa4197bd2a3/genomes/Hsapiens/hg19/bwa/hg19.fa.bwt -------------------------------------------------------------------------------- /genomes/Hsapiens/hg19/bwa/hg19.fa.pac: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/roryk/tiny-test-data/4dc37f0aaf5b2f3eec260a91689effa4197bd2a3/genomes/Hsapiens/hg19/bwa/hg19.fa.pac -------------------------------------------------------------------------------- /genomes/Hsapiens/hg19/bwa/hg19.fa.sa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/roryk/tiny-test-data/4dc37f0aaf5b2f3eec260a91689effa4197bd2a3/genomes/Hsapiens/hg19/bwa/hg19.fa.sa -------------------------------------------------------------------------------- /genomes/Hsapiens/hg19/rnaseq/ref-transcripts-mask.gtf: -------------------------------------------------------------------------------- 1 | chrM Mt_tRNA exon 577 647 . + . exon_number "1"; gene_id "ENSG00000210049"; exon_id "ENSE00001544501"; transcript_id "ENST00000387314"; gene_biotype "Mt_tRNA"; transcript_name "MT-TF-201"; gene_name "MT-TF"; 2 | chrM Mt_rRNA exon 648 1601 . + . exon_number "1"; gene_id "ENSG00000211459"; exon_id "ENSE00001544499"; transcript_id "ENST00000389680"; gene_biotype "Mt_rRNA"; transcript_name "MT-RNR1-201"; gene_name "MT-RNR1"; 3 | chrM Mt_tRNA exon 1602 1670 . + . exon_number "1"; gene_id "ENSG00000210077"; exon_id "ENSE00001544498"; transcript_id "ENST00000387342"; gene_biotype "Mt_tRNA"; transcript_name "MT-TV-201"; gene_name "MT-TV"; 4 | chrM Mt_rRNA exon 1671 3229 . + . exon_number "1"; gene_id "ENSG00000210082"; exon_id "ENSE00001544497"; transcript_id "ENST00000387347"; gene_biotype "Mt_rRNA"; transcript_name "MT-RNR2-201"; gene_name "MT-RNR2"; 5 | chrM Mt_tRNA exon 3230 3304 . + . exon_number "1"; gene_id "ENSG00000209082"; exon_id "ENSE00002006242"; transcript_id "ENST00000386347"; gene_biotype "Mt_tRNA"; transcript_name "MT-TL1-201"; gene_name "MT-TL1"; 6 | chrM Mt_tRNA exon 4263 4331 . + . exon_number "1"; gene_id "ENSG00000210100"; exon_id "ENSE00001993597"; transcript_id "ENST00000387365"; gene_biotype "Mt_tRNA"; transcript_name "MT-TI-201"; gene_name "MT-TI"; 7 | chrM Mt_tRNA exon 4329 4400 . - . exon_number "1"; gene_id "ENSG00000210107"; exon_id "ENSE00001544494"; transcript_id "ENST00000387372"; gene_biotype "Mt_tRNA"; transcript_name "MT-TQ-201"; gene_name "MT-TQ"; 8 | chrM Mt_tRNA exon 4402 4469 . + . exon_number "1"; gene_id "ENSG00000210112"; exon_id "ENSE00001544493"; transcript_id "ENST00000387377"; gene_biotype "Mt_tRNA"; transcript_name "MT-TM-201"; gene_name "MT-TM"; 9 | chrM Mt_tRNA exon 5512 5579 . + . exon_number "1"; gene_id "ENSG00000210117"; exon_id "ENSE00001544492"; transcript_id "ENST00000387382"; gene_biotype "Mt_tRNA"; transcript_name "MT-TW-201"; gene_name "MT-TW"; 10 | chrM Mt_tRNA exon 5587 5655 . - . exon_number "1"; gene_id "ENSG00000210127"; exon_id "ENSE00001544491"; transcript_id "ENST00000387392"; gene_biotype "Mt_tRNA"; transcript_name "MT-TA-201"; gene_name "MT-TA"; 11 | chrM Mt_tRNA exon 5657 5729 . - . exon_number "1"; gene_id "ENSG00000210135"; exon_id "ENSE00001544490"; transcript_id "ENST00000387400"; gene_biotype "Mt_tRNA"; transcript_name "MT-TN-201"; gene_name "MT-TN"; 12 | chrM Mt_tRNA exon 5761 5826 . - . exon_number "1"; gene_id "ENSG00000210140"; exon_id "ENSE00001544489"; transcript_id "ENST00000387405"; gene_biotype "Mt_tRNA"; transcript_name "MT-TC-201"; gene_name "MT-TC"; 13 | chrM Mt_tRNA exon 5826 5891 . - . exon_number "1"; gene_id "ENSG00000210144"; exon_id "ENSE00001544488"; transcript_id "ENST00000387409"; gene_biotype "Mt_tRNA"; transcript_name "MT-TY-201"; gene_name "MT-TY"; 14 | chrM Mt_tRNA exon 7446 7514 . - . exon_number "1"; gene_id "ENSG00000210151"; exon_id "ENSE00001544487"; transcript_id "ENST00000387416"; gene_biotype "Mt_tRNA"; transcript_name "MT-TS1-201"; gene_name "MT-TS1"; 15 | chrM Mt_tRNA exon 7518 7585 . + . exon_number "1"; gene_id "ENSG00000210154"; exon_id "ENSE00001544486"; transcript_id "ENST00000387419"; gene_biotype "Mt_tRNA"; transcript_name "MT-TD-201"; gene_name "MT-TD"; 16 | chrM Mt_tRNA exon 8295 8364 . + . exon_number "1"; gene_id "ENSG00000210156"; exon_id "ENSE00001544484"; transcript_id "ENST00000387421"; gene_biotype "Mt_tRNA"; transcript_name "MT-TK-201"; gene_name "MT-TK"; 17 | chrM Mt_tRNA exon 9991 10058 . + . exon_number "1"; gene_id "ENSG00000210164"; exon_id "ENSE00001544483"; transcript_id "ENST00000387429"; gene_biotype "Mt_tRNA"; transcript_name "MT-TG-201"; gene_name "MT-TG"; 18 | chrM Mt_tRNA exon 10405 10469 . + . exon_number "1"; gene_id "ENSG00000210174"; exon_id "ENSE00001544482"; transcript_id "ENST00000387439"; gene_biotype "Mt_tRNA"; transcript_name "MT-TR-201"; gene_name "MT-TR"; 19 | chrM Mt_tRNA exon 12138 12206 . + . exon_number "1"; gene_id "ENSG00000210176"; exon_id "ENSE00001544480"; transcript_id "ENST00000387441"; gene_biotype "Mt_tRNA"; transcript_name "MT-TH-201"; gene_name "MT-TH"; 20 | chrM Mt_tRNA exon 12207 12265 . + . exon_number "1"; gene_id "ENSG00000210184"; exon_id "ENSE00001544479"; transcript_id "ENST00000387449"; gene_biotype "Mt_tRNA"; transcript_name "MT-TS2-201"; gene_name "MT-TS2"; 21 | chrM Mt_tRNA exon 12266 12336 . + . exon_number "1"; gene_id "ENSG00000210191"; exon_id "ENSE00001544478"; transcript_id "ENST00000387456"; gene_biotype "Mt_tRNA"; transcript_name "MT-TL2-201"; gene_name "MT-TL2"; 22 | chrM Mt_tRNA exon 14674 14742 . - . exon_number "1"; gene_id "ENSG00000210194"; exon_id "ENSE00001544476"; transcript_id "ENST00000387459"; gene_biotype "Mt_tRNA"; transcript_name "MT-TE-201"; gene_name "MT-TE"; 23 | chrM Mt_tRNA exon 15888 15953 . + . exon_number "1"; gene_id "ENSG00000210195"; exon_id "ENSE00001544475"; transcript_id "ENST00000387460"; gene_biotype "Mt_tRNA"; transcript_name "MT-TT-201"; gene_name "MT-TT"; 24 | chrM Mt_tRNA exon 15956 16023 . - . exon_number "1"; gene_id "ENSG00000210196"; exon_id "ENSE00001544473"; transcript_id "ENST00000387461"; gene_biotype "Mt_tRNA"; transcript_name "MT-TP-201"; gene_name "MT-TP"; 25 | -------------------------------------------------------------------------------- /genomes/Hsapiens/hg19/rnaseq/ref-transcripts.bed: -------------------------------------------------------------------------------- 1 | chrM 577 647 MT-TF . + 2 | chrM 648 1601 MT-RNR1 . + 3 | chrM 1602 1670 MT-TV . + 4 | chrM 1671 3229 MT-RNR2 . + 5 | chrM 3230 3304 MT-TL1 . + 6 | chrM 3307 4262 MT-ND1 . + 7 | chrM 3307 4262 MT-ND1 . + 8 | chrM 3307 3309 MT-ND1 . + 9 | chrM 4263 4331 MT-TI . + 10 | chrM 4329 4400 MT-TQ . - 11 | chrM 4402 4469 MT-TM . + 12 | chrM 4470 5511 MT-ND2 . + 13 | chrM 4470 5511 MT-ND2 . + 14 | chrM 4470 4472 MT-ND2 . + 15 | chrM 5512 5579 MT-TW . + 16 | chrM 5587 5655 MT-TA . - 17 | chrM 5657 5729 MT-TN . - 18 | chrM 5761 5826 MT-TC . - 19 | chrM 5826 5891 MT-TY . - 20 | chrM 5904 7445 MT-CO1 . + 21 | chrM 5904 7442 MT-CO1 . + 22 | chrM 5904 5906 MT-CO1 . + 23 | chrM 7443 7445 MT-CO1 . + 24 | chrM 7446 7514 MT-TS1 . - 25 | chrM 7518 7585 MT-TD . + 26 | chrM 7586 8269 MT-CO2 . + 27 | chrM 7586 8266 MT-CO2 . + 28 | chrM 7586 7588 MT-CO2 . + 29 | chrM 8267 8269 MT-CO2 . + 30 | chrM 8295 8364 MT-TK . + 31 | chrM 8366 8572 MT-ATP8 . + 32 | chrM 8366 8569 MT-ATP8 . + 33 | chrM 8366 8368 MT-ATP8 . + 34 | chrM 8570 8572 MT-ATP8 . + 35 | chrM 8527 9207 MT-ATP6 . + 36 | chrM 8527 9204 MT-ATP6 . + 37 | chrM 8527 8529 MT-ATP6 . + 38 | chrM 9205 9207 MT-ATP6 . + 39 | chrM 9207 9990 MT-CO3 . + 40 | chrM 9207 9990 MT-CO3 . + 41 | chrM 9207 9209 MT-CO3 . + 42 | chrM 9991 10058 MT-TG . + 43 | chrM 10059 10404 MT-ND3 . + 44 | chrM 10059 10404 MT-ND3 . + 45 | chrM 10059 10061 MT-ND3 . + 46 | chrM 10405 10469 MT-TR . + 47 | chrM 10470 10766 MT-ND4L . + 48 | chrM 10470 10763 MT-ND4L . + 49 | chrM 10470 10472 MT-ND4L . + 50 | chrM 10764 10766 MT-ND4L . + 51 | chrM 10760 12137 MT-ND4 . + 52 | chrM 10760 12137 MT-ND4 . + 53 | chrM 10760 10762 MT-ND4 . + 54 | chrM 12138 12206 MT-TH . + 55 | chrM 12207 12265 MT-TS2 . + 56 | chrM 12266 12336 MT-TL2 . + 57 | chrM 12337 14148 MT-ND5 . + 58 | chrM 12337 14145 MT-ND5 . + 59 | chrM 12337 12339 MT-ND5 . + 60 | chrM 14146 14148 MT-ND5 . + 61 | chrM 14149 14673 MT-ND6 . - 62 | chrM 14152 14673 MT-ND6 . - 63 | chrM 14671 14673 MT-ND6 . - 64 | chrM 14149 14151 MT-ND6 . - 65 | chrM 14674 14742 MT-TE . - 66 | chrM 14747 15887 MT-CYB . + 67 | chrM 14747 15887 MT-CYB . + 68 | chrM 14747 14749 MT-CYB . + 69 | chrM 15888 15953 MT-TT . + 70 | chrM 15956 16023 MT-TP . - 71 | -------------------------------------------------------------------------------- /genomes/Hsapiens/hg19/rnaseq/ref-transcripts.gtf: -------------------------------------------------------------------------------- 1 | chrM Mt_tRNA exon 577 647 . + . gene_id "ENSG00000210049"; transcript_id "ENST00000387314"; exon_number "1"; gene_name "MT-TF"; gene_biotype "Mt_tRNA"; transcript_name "MT-TF-201"; exon_id "ENSE00001544501"; 2 | chrM Mt_rRNA exon 648 1601 . + . gene_id "ENSG00000211459"; transcript_id "ENST00000389680"; exon_number "1"; gene_name "MT-RNR1"; gene_biotype "Mt_rRNA"; transcript_name "MT-RNR1-201"; exon_id "ENSE00001544499"; 3 | chrM Mt_tRNA exon 1602 1670 . + . gene_id "ENSG00000210077"; transcript_id "ENST00000387342"; exon_number "1"; gene_name "MT-TV"; gene_biotype "Mt_tRNA"; transcript_name "MT-TV-201"; exon_id "ENSE00001544498"; 4 | chrM Mt_rRNA exon 1671 3229 . + . gene_id "ENSG00000210082"; transcript_id "ENST00000387347"; exon_number "1"; gene_name "MT-RNR2"; gene_biotype "Mt_rRNA"; transcript_name "MT-RNR2-201"; exon_id "ENSE00001544497"; 5 | chrM Mt_tRNA exon 3230 3304 . + . gene_id "ENSG00000209082"; transcript_id "ENST00000386347"; exon_number "1"; gene_name "MT-TL1"; gene_biotype "Mt_tRNA"; transcript_name "MT-TL1-201"; exon_id "ENSE00002006242"; 6 | chrM protein_coding exon 3307 4262 . + . gene_id "ENSG00000198888"; transcript_id "ENST00000361390"; exon_number "1"; gene_name "MT-ND1"; gene_biotype "protein_coding"; transcript_name "MT-ND1-201"; exon_id "ENSE00001435714"; 7 | chrM protein_coding CDS 3307 4262 . + 0 gene_id "ENSG00000198888"; transcript_id "ENST00000361390"; exon_number "1"; gene_name "MT-ND1"; gene_biotype "protein_coding"; transcript_name "MT-ND1-201"; protein_id "ENSP00000354687"; 8 | chrM protein_coding start_codon 3307 3309 . + 0 gene_id "ENSG00000198888"; transcript_id "ENST00000361390"; exon_number "1"; gene_name "MT-ND1"; gene_biotype "protein_coding"; transcript_name "MT-ND1-201"; 9 | chrM Mt_tRNA exon 4263 4331 . + . gene_id "ENSG00000210100"; transcript_id "ENST00000387365"; exon_number "1"; gene_name "MT-TI"; gene_biotype "Mt_tRNA"; transcript_name "MT-TI-201"; exon_id "ENSE00001993597"; 10 | chrM Mt_tRNA exon 4329 4400 . - . gene_id "ENSG00000210107"; transcript_id "ENST00000387372"; exon_number "1"; gene_name "MT-TQ"; gene_biotype "Mt_tRNA"; transcript_name "MT-TQ-201"; exon_id "ENSE00001544494"; 11 | chrM Mt_tRNA exon 4402 4469 . + . gene_id "ENSG00000210112"; transcript_id "ENST00000387377"; exon_number "1"; gene_name "MT-TM"; gene_biotype "Mt_tRNA"; transcript_name "MT-TM-201"; exon_id "ENSE00001544493"; 12 | chrM protein_coding exon 4470 5511 . + . gene_id "ENSG00000198763"; transcript_id "ENST00000361453"; exon_number "1"; gene_name "MT-ND2"; gene_biotype "protein_coding"; transcript_name "MT-ND2-201"; exon_id "ENSE00001435686"; 13 | chrM protein_coding CDS 4470 5511 . + 0 gene_id "ENSG00000198763"; transcript_id "ENST00000361453"; exon_number "1"; gene_name "MT-ND2"; gene_biotype "protein_coding"; transcript_name "MT-ND2-201"; protein_id "ENSP00000355046"; 14 | chrM protein_coding start_codon 4470 4472 . + 0 gene_id "ENSG00000198763"; transcript_id "ENST00000361453"; exon_number "1"; gene_name "MT-ND2"; gene_biotype "protein_coding"; transcript_name "MT-ND2-201"; 15 | chrM Mt_tRNA exon 5512 5579 . + . gene_id "ENSG00000210117"; transcript_id "ENST00000387382"; exon_number "1"; gene_name "MT-TW"; gene_biotype "Mt_tRNA"; transcript_name "MT-TW-201"; exon_id "ENSE00001544492"; 16 | chrM Mt_tRNA exon 5587 5655 . - . gene_id "ENSG00000210127"; transcript_id "ENST00000387392"; exon_number "1"; gene_name "MT-TA"; gene_biotype "Mt_tRNA"; transcript_name "MT-TA-201"; exon_id "ENSE00001544491"; 17 | chrM Mt_tRNA exon 5657 5729 . - . gene_id "ENSG00000210135"; transcript_id "ENST00000387400"; exon_number "1"; gene_name "MT-TN"; gene_biotype "Mt_tRNA"; transcript_name "MT-TN-201"; exon_id "ENSE00001544490"; 18 | chrM Mt_tRNA exon 5761 5826 . - . gene_id "ENSG00000210140"; transcript_id "ENST00000387405"; exon_number "1"; gene_name "MT-TC"; gene_biotype "Mt_tRNA"; transcript_name "MT-TC-201"; exon_id "ENSE00001544489"; 19 | chrM Mt_tRNA exon 5826 5891 . - . gene_id "ENSG00000210144"; transcript_id "ENST00000387409"; exon_number "1"; gene_name "MT-TY"; gene_biotype "Mt_tRNA"; transcript_name "MT-TY-201"; exon_id "ENSE00001544488"; 20 | chrM protein_coding exon 5904 7445 . + . gene_id "ENSG00000198804"; transcript_id "ENST00000361624"; exon_number "1"; gene_name "MT-CO1"; gene_biotype "protein_coding"; transcript_name "MT-CO1-201"; exon_id "ENSE00001435647"; 21 | chrM protein_coding CDS 5904 7442 . + 0 gene_id "ENSG00000198804"; transcript_id "ENST00000361624"; exon_number "1"; gene_name "MT-CO1"; gene_biotype "protein_coding"; transcript_name "MT-CO1-201"; protein_id "ENSP00000354499"; 22 | chrM protein_coding start_codon 5904 5906 . + 0 gene_id "ENSG00000198804"; transcript_id "ENST00000361624"; exon_number "1"; gene_name "MT-CO1"; gene_biotype "protein_coding"; transcript_name "MT-CO1-201"; 23 | chrM protein_coding stop_codon 7443 7445 . + 0 gene_id "ENSG00000198804"; transcript_id "ENST00000361624"; exon_number "1"; gene_name "MT-CO1"; gene_biotype "protein_coding"; transcript_name "MT-CO1-201"; 24 | chrM Mt_tRNA exon 7446 7514 . - . gene_id "ENSG00000210151"; transcript_id "ENST00000387416"; exon_number "1"; gene_name "MT-TS1"; gene_biotype "Mt_tRNA"; transcript_name "MT-TS1-201"; exon_id "ENSE00001544487"; 25 | chrM Mt_tRNA exon 7518 7585 . + . gene_id "ENSG00000210154"; transcript_id "ENST00000387419"; exon_number "1"; gene_name "MT-TD"; gene_biotype "Mt_tRNA"; transcript_name "MT-TD-201"; exon_id "ENSE00001544486"; 26 | chrM protein_coding exon 7586 8269 . + . gene_id "ENSG00000198712"; transcript_id "ENST00000361739"; exon_number "1"; gene_name "MT-CO2"; gene_biotype "protein_coding"; transcript_name "MT-CO2-201"; exon_id "ENSE00001435613"; 27 | chrM protein_coding CDS 7586 8266 . + 0 gene_id "ENSG00000198712"; transcript_id "ENST00000361739"; exon_number "1"; gene_name "MT-CO2"; gene_biotype "protein_coding"; transcript_name "MT-CO2-201"; protein_id "ENSP00000354876"; 28 | chrM protein_coding start_codon 7586 7588 . + 0 gene_id "ENSG00000198712"; transcript_id "ENST00000361739"; exon_number "1"; gene_name "MT-CO2"; gene_biotype "protein_coding"; transcript_name "MT-CO2-201"; 29 | chrM protein_coding stop_codon 8267 8269 . + 0 gene_id "ENSG00000198712"; transcript_id "ENST00000361739"; exon_number "1"; gene_name "MT-CO2"; gene_biotype "protein_coding"; transcript_name "MT-CO2-201"; 30 | chrM Mt_tRNA exon 8295 8364 . + . gene_id "ENSG00000210156"; transcript_id "ENST00000387421"; exon_number "1"; gene_name "MT-TK"; gene_biotype "Mt_tRNA"; transcript_name "MT-TK-201"; exon_id "ENSE00001544484"; 31 | chrM protein_coding exon 8366 8572 . + . gene_id "ENSG00000228253"; transcript_id "ENST00000361851"; exon_number "1"; gene_name "MT-ATP8"; gene_biotype "protein_coding"; transcript_name "MT-ATP8-201"; exon_id "ENSE00001435286"; 32 | chrM protein_coding CDS 8366 8569 . + 0 gene_id "ENSG00000228253"; transcript_id "ENST00000361851"; exon_number "1"; gene_name "MT-ATP8"; gene_biotype "protein_coding"; transcript_name "MT-ATP8-201"; protein_id "ENSP00000355265"; 33 | chrM protein_coding start_codon 8366 8368 . + 0 gene_id "ENSG00000228253"; transcript_id "ENST00000361851"; exon_number "1"; gene_name "MT-ATP8"; gene_biotype "protein_coding"; transcript_name "MT-ATP8-201"; 34 | chrM protein_coding stop_codon 8570 8572 . + 0 gene_id "ENSG00000228253"; transcript_id "ENST00000361851"; exon_number "1"; gene_name "MT-ATP8"; gene_biotype "protein_coding"; transcript_name "MT-ATP8-201"; 35 | chrM protein_coding exon 8527 9207 . + . gene_id "ENSG00000198899"; transcript_id "ENST00000361899"; exon_number "1"; gene_name "MT-ATP6"; gene_biotype "protein_coding"; transcript_name "MT-ATP6-201"; exon_id "ENSE00001727012"; 36 | chrM protein_coding CDS 8527 9204 . + 0 gene_id "ENSG00000198899"; transcript_id "ENST00000361899"; exon_number "1"; gene_name "MT-ATP6"; gene_biotype "protein_coding"; transcript_name "MT-ATP6-201"; protein_id "ENSP00000354632"; 37 | chrM protein_coding start_codon 8527 8529 . + 0 gene_id "ENSG00000198899"; transcript_id "ENST00000361899"; exon_number "1"; gene_name "MT-ATP6"; gene_biotype "protein_coding"; transcript_name "MT-ATP6-201"; 38 | chrM protein_coding stop_codon 9205 9207 . + 0 gene_id "ENSG00000198899"; transcript_id "ENST00000361899"; exon_number "1"; gene_name "MT-ATP6"; gene_biotype "protein_coding"; transcript_name "MT-ATP6-201"; 39 | chrM protein_coding exon 9207 9990 . + . gene_id "ENSG00000198938"; transcript_id "ENST00000362079"; exon_number "1"; gene_name "MT-CO3"; gene_biotype "protein_coding"; transcript_name "MT-CO3-201"; exon_id "ENSE00001608952"; 40 | chrM protein_coding CDS 9207 9990 . + 0 gene_id "ENSG00000198938"; transcript_id "ENST00000362079"; exon_number "1"; gene_name "MT-CO3"; gene_biotype "protein_coding"; transcript_name "MT-CO3-201"; protein_id "ENSP00000354982"; 41 | chrM protein_coding start_codon 9207 9209 . + 0 gene_id "ENSG00000198938"; transcript_id "ENST00000362079"; exon_number "1"; gene_name "MT-CO3"; gene_biotype "protein_coding"; transcript_name "MT-CO3-201"; 42 | chrM Mt_tRNA exon 9991 10058 . + . gene_id "ENSG00000210164"; transcript_id "ENST00000387429"; exon_number "1"; gene_name "MT-TG"; gene_biotype "Mt_tRNA"; transcript_name "MT-TG-201"; exon_id "ENSE00001544483"; 43 | chrM protein_coding exon 10059 10404 . + . gene_id "ENSG00000198840"; transcript_id "ENST00000361227"; exon_number "1"; gene_name "MT-ND3"; gene_biotype "protein_coding"; transcript_name "MT-ND3-201"; exon_id "ENSE00001435444"; 44 | chrM protein_coding CDS 10059 10404 . + 0 gene_id "ENSG00000198840"; transcript_id "ENST00000361227"; exon_number "1"; gene_name "MT-ND3"; gene_biotype "protein_coding"; transcript_name "MT-ND3-201"; protein_id "ENSP00000355206"; 45 | chrM protein_coding start_codon 10059 10061 . + 0 gene_id "ENSG00000198840"; transcript_id "ENST00000361227"; exon_number "1"; gene_name "MT-ND3"; gene_biotype "protein_coding"; transcript_name "MT-ND3-201"; 46 | chrM Mt_tRNA exon 10405 10469 . + . gene_id "ENSG00000210174"; transcript_id "ENST00000387439"; exon_number "1"; gene_name "MT-TR"; gene_biotype "Mt_tRNA"; transcript_name "MT-TR-201"; exon_id "ENSE00001544482"; 47 | chrM protein_coding exon 10470 10766 . + . gene_id "ENSG00000212907"; transcript_id "ENST00000361335"; exon_number "1"; gene_name "MT-ND4L"; gene_biotype "protein_coding"; transcript_name "MT-ND4L-201"; exon_id "ENSE00001596097"; 48 | chrM protein_coding CDS 10470 10763 . + 0 gene_id "ENSG00000212907"; transcript_id "ENST00000361335"; exon_number "1"; gene_name "MT-ND4L"; gene_biotype "protein_coding"; transcript_name "MT-ND4L-201"; protein_id "ENSP00000354728"; 49 | chrM protein_coding start_codon 10470 10472 . + 0 gene_id "ENSG00000212907"; transcript_id "ENST00000361335"; exon_number "1"; gene_name "MT-ND4L"; gene_biotype "protein_coding"; transcript_name "MT-ND4L-201"; 50 | chrM protein_coding stop_codon 10764 10766 . + 0 gene_id "ENSG00000212907"; transcript_id "ENST00000361335"; exon_number "1"; gene_name "MT-ND4L"; gene_biotype "protein_coding"; transcript_name "MT-ND4L-201"; 51 | chrM protein_coding exon 10760 12137 . + . gene_id "ENSG00000198886"; transcript_id "ENST00000361381"; exon_number "1"; gene_name "MT-ND4"; gene_biotype "protein_coding"; transcript_name "MT-ND4-201"; exon_id "ENSE00001666004"; 52 | chrM protein_coding CDS 10760 12137 . + 0 gene_id "ENSG00000198886"; transcript_id "ENST00000361381"; exon_number "1"; gene_name "MT-ND4"; gene_biotype "protein_coding"; transcript_name "MT-ND4-201"; protein_id "ENSP00000354961"; 53 | chrM protein_coding start_codon 10760 10762 . + 0 gene_id "ENSG00000198886"; transcript_id "ENST00000361381"; exon_number "1"; gene_name "MT-ND4"; gene_biotype "protein_coding"; transcript_name "MT-ND4-201"; 54 | chrM Mt_tRNA exon 12138 12206 . + . gene_id "ENSG00000210176"; transcript_id "ENST00000387441"; exon_number "1"; gene_name "MT-TH"; gene_biotype "Mt_tRNA"; transcript_name "MT-TH-201"; exon_id "ENSE00001544480"; 55 | chrM Mt_tRNA exon 12207 12265 . + . gene_id "ENSG00000210184"; transcript_id "ENST00000387449"; exon_number "1"; gene_name "MT-TS2"; gene_biotype "Mt_tRNA"; transcript_name "MT-TS2-201"; exon_id "ENSE00001544479"; 56 | chrM Mt_tRNA exon 12266 12336 . + . gene_id "ENSG00000210191"; transcript_id "ENST00000387456"; exon_number "1"; gene_name "MT-TL2"; gene_biotype "Mt_tRNA"; transcript_name "MT-TL2-201"; exon_id "ENSE00001544478"; 57 | chrM protein_coding exon 12337 14148 . + . gene_id "ENSG00000198786"; transcript_id "ENST00000361567"; exon_number "1"; gene_name "MT-ND5"; gene_biotype "protein_coding"; transcript_name "MT-ND5-201"; exon_id "ENSE00001435330"; 58 | chrM protein_coding CDS 12337 14145 . + 0 gene_id "ENSG00000198786"; transcript_id "ENST00000361567"; exon_number "1"; gene_name "MT-ND5"; gene_biotype "protein_coding"; transcript_name "MT-ND5-201"; protein_id "ENSP00000354813"; 59 | chrM protein_coding start_codon 12337 12339 . + 0 gene_id "ENSG00000198786"; transcript_id "ENST00000361567"; exon_number "1"; gene_name "MT-ND5"; gene_biotype "protein_coding"; transcript_name "MT-ND5-201"; 60 | chrM protein_coding stop_codon 14146 14148 . + 0 gene_id "ENSG00000198786"; transcript_id "ENST00000361567"; exon_number "1"; gene_name "MT-ND5"; gene_biotype "protein_coding"; transcript_name "MT-ND5-201"; 61 | chrM protein_coding exon 14149 14673 . - . gene_id "ENSG00000198695"; transcript_id "ENST00000361681"; exon_number "1"; gene_name "MT-ND6"; gene_biotype "protein_coding"; transcript_name "MT-ND6-201"; exon_id "ENSE00001434974"; 62 | chrM protein_coding CDS 14152 14673 . - 0 gene_id "ENSG00000198695"; transcript_id "ENST00000361681"; exon_number "1"; gene_name "MT-ND6"; gene_biotype "protein_coding"; transcript_name "MT-ND6-201"; protein_id "ENSP00000354665"; 63 | chrM protein_coding start_codon 14671 14673 . - 0 gene_id "ENSG00000198695"; transcript_id "ENST00000361681"; exon_number "1"; gene_name "MT-ND6"; gene_biotype "protein_coding"; transcript_name "MT-ND6-201"; 64 | chrM protein_coding stop_codon 14149 14151 . - 0 gene_id "ENSG00000198695"; transcript_id "ENST00000361681"; exon_number "1"; gene_name "MT-ND6"; gene_biotype "protein_coding"; transcript_name "MT-ND6-201"; 65 | chrM Mt_tRNA exon 14674 14742 . - . gene_id "ENSG00000210194"; transcript_id "ENST00000387459"; exon_number "1"; gene_name "MT-TE"; gene_biotype "Mt_tRNA"; transcript_name "MT-TE-201"; exon_id "ENSE00001544476"; 66 | chrM protein_coding exon 14747 15887 . + . gene_id "ENSG00000198727"; transcript_id "ENST00000361789"; exon_number "1"; gene_name "MT-CYB"; gene_biotype "protein_coding"; transcript_name "MT-CYB-201"; exon_id "ENSE00001436074"; 67 | chrM protein_coding CDS 14747 15887 . + 0 gene_id "ENSG00000198727"; transcript_id "ENST00000361789"; exon_number "1"; gene_name "MT-CYB"; gene_biotype "protein_coding"; transcript_name "MT-CYB-201"; protein_id "ENSP00000354554"; 68 | chrM protein_coding start_codon 14747 14749 . + 0 gene_id "ENSG00000198727"; transcript_id "ENST00000361789"; exon_number "1"; gene_name "MT-CYB"; gene_biotype "protein_coding"; transcript_name "MT-CYB-201"; 69 | chrM Mt_tRNA exon 15888 15953 . + . gene_id "ENSG00000210195"; transcript_id "ENST00000387460"; exon_number "1"; gene_name "MT-TT"; gene_biotype "Mt_tRNA"; transcript_name "MT-TT-201"; exon_id "ENSE00001544475"; 70 | chrM Mt_tRNA exon 15956 16023 . - . gene_id "ENSG00000210196"; transcript_id "ENST00000387461"; exon_number "1"; gene_name "MT-TP"; gene_biotype "Mt_tRNA"; transcript_name "MT-TP-201"; exon_id "ENSE00001544473"; 71 | -------------------------------------------------------------------------------- /genomes/Hsapiens/hg19/rnaseq/ref-transcripts.refflat: -------------------------------------------------------------------------------- 1 | ENST00000387314 ENST00000387314 chrM + 576 647 647 647 1 576, 647, 0 ENSG00000210049 none none -1, 2 | ENST00000389680 ENST00000389680 chrM + 647 1601 1601 1601 1 647, 1601, 0 ENSG00000211459 none none -1, 3 | ENST00000387342 ENST00000387342 chrM + 1601 1670 1670 1670 1 1601, 1670, 0 ENSG00000210077 none none -1, 4 | ENST00000387347 ENST00000387347 chrM + 1670 3229 3229 3229 1 1670, 3229, 0 ENSG00000210082 none none -1, 5 | ENST00000386347 ENST00000386347 chrM + 3229 3304 3304 3304 1 3229, 3304, 0 ENSG00000209082 none none -1, 6 | ENST00000361390 ENST00000361390 chrM + 3306 4262 3306 4262 1 3306, 4262, 0 ENSG00000198888 cmpl incmpl 0, 7 | ENST00000387365 ENST00000387365 chrM + 4262 4331 4331 4331 1 4262, 4331, 0 ENSG00000210100 none none -1, 8 | ENST00000387372 ENST00000387372 chrM - 4328 4400 4400 4400 1 4328, 4400, 0 ENSG00000210107 none none -1, 9 | ENST00000387377 ENST00000387377 chrM + 4401 4469 4469 4469 1 4401, 4469, 0 ENSG00000210112 none none -1, 10 | ENST00000361453 ENST00000361453 chrM + 4469 5511 4469 5511 1 4469, 5511, 0 ENSG00000198763 cmpl incmpl 0, 11 | ENST00000387382 ENST00000387382 chrM + 5511 5579 5579 5579 1 5511, 5579, 0 ENSG00000210117 none none -1, 12 | ENST00000387392 ENST00000387392 chrM - 5586 5655 5655 5655 1 5586, 5655, 0 ENSG00000210127 none none -1, 13 | ENST00000387400 ENST00000387400 chrM - 5656 5729 5729 5729 1 5656, 5729, 0 ENSG00000210135 none none -1, 14 | ENST00000387405 ENST00000387405 chrM - 5760 5826 5826 5826 1 5760, 5826, 0 ENSG00000210140 none none -1, 15 | ENST00000387409 ENST00000387409 chrM - 5825 5891 5891 5891 1 5825, 5891, 0 ENSG00000210144 none none -1, 16 | ENST00000361624 ENST00000361624 chrM + 5903 7445 5903 7445 1 5903, 7445, 0 ENSG00000198804 cmpl cmpl 0, 17 | ENST00000387416 ENST00000387416 chrM - 7445 7514 7514 7514 1 7445, 7514, 0 ENSG00000210151 none none -1, 18 | ENST00000387419 ENST00000387419 chrM + 7517 7585 7585 7585 1 7517, 7585, 0 ENSG00000210154 none none -1, 19 | ENST00000361739 ENST00000361739 chrM + 7585 8269 7585 8269 1 7585, 8269, 0 ENSG00000198712 cmpl cmpl 0, 20 | ENST00000387421 ENST00000387421 chrM + 8294 8364 8364 8364 1 8294, 8364, 0 ENSG00000210156 none none -1, 21 | ENST00000361851 ENST00000361851 chrM + 8365 8572 8365 8572 1 8365, 8572, 0 ENSG00000228253 cmpl cmpl 0, 22 | ENST00000361899 ENST00000361899 chrM + 8526 9207 8526 9207 1 8526, 9207, 0 ENSG00000198899 cmpl cmpl 0, 23 | ENST00000362079 ENST00000362079 chrM + 9206 9990 9206 9990 1 9206, 9990, 0 ENSG00000198938 cmpl incmpl 0, 24 | ENST00000387429 ENST00000387429 chrM + 9990 10058 10058 10058 1 9990, 10058, 0 ENSG00000210164 none none -1, 25 | ENST00000361227 ENST00000361227 chrM + 10058 10404 10058 10404 1 10058, 10404, 0 ENSG00000198840 cmpl incmpl 0, 26 | ENST00000387439 ENST00000387439 chrM + 10404 10469 10469 10469 1 10404, 10469, 0 ENSG00000210174 none none -1, 27 | ENST00000361335 ENST00000361335 chrM + 10469 10766 10469 10766 1 10469, 10766, 0 ENSG00000212907 cmpl cmpl 0, 28 | ENST00000361381 ENST00000361381 chrM + 10759 12137 10759 12137 1 10759, 12137, 0 ENSG00000198886 cmpl incmpl 0, 29 | ENST00000387441 ENST00000387441 chrM + 12137 12206 12206 12206 1 12137, 12206, 0 ENSG00000210176 none none -1, 30 | ENST00000387449 ENST00000387449 chrM + 12206 12265 12265 12265 1 12206, 12265, 0 ENSG00000210184 none none -1, 31 | ENST00000387456 ENST00000387456 chrM + 12265 12336 12336 12336 1 12265, 12336, 0 ENSG00000210191 none none -1, 32 | ENST00000361567 ENST00000361567 chrM + 12336 14148 12336 14148 1 12336, 14148, 0 ENSG00000198786 cmpl cmpl 0, 33 | ENST00000361681 ENST00000361681 chrM - 14148 14673 14148 14673 1 14148, 14673, 0 ENSG00000198695 cmpl cmpl 0, 34 | ENST00000387459 ENST00000387459 chrM - 14673 14742 14742 14742 1 14673, 14742, 0 ENSG00000210194 none none -1, 35 | ENST00000361789 ENST00000361789 chrM + 14746 15887 14746 15887 1 14746, 15887, 0 ENSG00000198727 cmpl incmpl 0, 36 | ENST00000387460 ENST00000387460 chrM + 15887 15953 15953 15953 1 15887, 15953, 0 ENSG00000210195 none none -1, 37 | ENST00000387461 ENST00000387461 chrM - 15955 16023 16023 16023 1 15955, 16023, 0 ENSG00000210196 none none -1, 38 | -------------------------------------------------------------------------------- /genomes/Hsapiens/hg19/seq/hg19-resources.yaml: -------------------------------------------------------------------------------- 1 | version: 1 2 | 3 | aliases: 4 | human: true 5 | snpeff: hg19 6 | ensembl: human 7 | 8 | variation: 9 | dbsnp: ../variation/dbsnp_132.vcf 10 | train_hapmap: ../variation/hapmap_3.3.vcf 11 | train_1000g_omni: ../variation/1000G_omni2.5.vcf 12 | train_indels: ../variation/Mills_Devine_2hit.indels.vcf 13 | 14 | rnaseq: 15 | transcripts: ../rnaseq/ref-transcripts.gtf 16 | transcripts_mask: ../rnaseq/ref-transcripts-mask.gtf -------------------------------------------------------------------------------- /genomes/Hsapiens/hg19/seq/hg19.dict: -------------------------------------------------------------------------------- 1 | @HD VN:1.0 SO:unsorted 2 | @SQ SN:chrM LN:16571 UR:file:/home/bchapman/bio/bcbb/nextgen/tests/data/automated/tool-data/../../genomes/hg19/seq/hg19.fa M5:d2ed829b8a1628d16cbeee88e88e39eb 3 | @SQ SN:chr22 LN:20001 UR:file:/home/bchapman/bio/bcbb/nextgen/tests/data/automated/tool-data/../../genomes/hg19/seq/hg19.fa M5:1b07f9698158e44bcfebeaaa6f7908a0 4 | -------------------------------------------------------------------------------- /genomes/Hsapiens/hg19/seq/hg19.fa.fai: -------------------------------------------------------------------------------- 1 | chrM 16571 6 60 61 2 | chr22 20001 16861 60 61 3 | -------------------------------------------------------------------------------- /genomes/Hsapiens/hg19/ucsc/hg19.2bit: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/roryk/tiny-test-data/4dc37f0aaf5b2f3eec260a91689effa4197bd2a3/genomes/Hsapiens/hg19/ucsc/hg19.2bit -------------------------------------------------------------------------------- /genomes/Mmusculus/mm9/bowtie2/mm9.1.bt2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/roryk/tiny-test-data/4dc37f0aaf5b2f3eec260a91689effa4197bd2a3/genomes/Mmusculus/mm9/bowtie2/mm9.1.bt2 -------------------------------------------------------------------------------- /genomes/Mmusculus/mm9/bowtie2/mm9.2.bt2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/roryk/tiny-test-data/4dc37f0aaf5b2f3eec260a91689effa4197bd2a3/genomes/Mmusculus/mm9/bowtie2/mm9.2.bt2 -------------------------------------------------------------------------------- /genomes/Mmusculus/mm9/bowtie2/mm9.3.bt2: 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/genomes/Mmusculus/mm9/bowtie2/mm9.rev.2.bt2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/roryk/tiny-test-data/4dc37f0aaf5b2f3eec260a91689effa4197bd2a3/genomes/Mmusculus/mm9/bowtie2/mm9.rev.2.bt2 -------------------------------------------------------------------------------- /genomes/Mmusculus/mm9/bwa/mm9.fa.amb: -------------------------------------------------------------------------------- 1 | 16299 1 0 2 | -------------------------------------------------------------------------------- /genomes/Mmusculus/mm9/bwa/mm9.fa.ann: -------------------------------------------------------------------------------- 1 | 16299 1 11 2 | 0 chrM (null) 3 | 0 16299 0 4 | -------------------------------------------------------------------------------- /genomes/Mmusculus/mm9/bwa/mm9.fa.bwt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/roryk/tiny-test-data/4dc37f0aaf5b2f3eec260a91689effa4197bd2a3/genomes/Mmusculus/mm9/bwa/mm9.fa.bwt -------------------------------------------------------------------------------- /genomes/Mmusculus/mm9/bwa/mm9.fa.pac: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/roryk/tiny-test-data/4dc37f0aaf5b2f3eec260a91689effa4197bd2a3/genomes/Mmusculus/mm9/bwa/mm9.fa.pac -------------------------------------------------------------------------------- /genomes/Mmusculus/mm9/bwa/mm9.fa.sa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/roryk/tiny-test-data/4dc37f0aaf5b2f3eec260a91689effa4197bd2a3/genomes/Mmusculus/mm9/bwa/mm9.fa.sa -------------------------------------------------------------------------------- /genomes/Mmusculus/mm9/rnaseq/ref-transcripts-mask.gtf: -------------------------------------------------------------------------------- 1 | chrM Mt_rRNA exon 70 1024 . + . gene_id "ENSMUSG00000064337"; transcript_id "ENSMUST00000082388"; exon_number "1"; gene_name "mt-Rnr1"; transcript_name "mt-Rnr1-201"; 2 | chrM Mt_rRNA exon 1094 2675 . + . gene_id "ENSMUSG00000064339"; transcript_id "ENSMUST00000082390"; exon_number "1"; gene_name "mt-Rnr2"; transcript_name "mt-Rnr2-201"; 3 | -------------------------------------------------------------------------------- /genomes/Mmusculus/mm9/rnaseq/ref-transcripts.gtf: -------------------------------------------------------------------------------- 1 | chrM Mt_tRNA exon 1 68 . + . gene_id "ENSMUSG00000064336"; transcript_id "ENSMUST00000082387"; exon_number "1"; gene_name "mt-Tf"; transcript_name "mt-Tf-201"; 2 | chrM Mt_rRNA exon 70 1024 . + . gene_id "ENSMUSG00000064337"; transcript_id "ENSMUST00000082388"; exon_number "1"; gene_name "mt-Rnr1"; transcript_name "mt-Rnr1-201"; 3 | chrM Mt_tRNA exon 1025 1093 . + . gene_id "ENSMUSG00000064338"; transcript_id "ENSMUST00000082389"; exon_number "1"; gene_name "mt-Tv"; transcript_name "mt-Tv-201"; 4 | chrM Mt_rRNA exon 1094 2675 . + . gene_id "ENSMUSG00000064339"; transcript_id "ENSMUST00000082390"; exon_number "1"; gene_name "mt-Rnr2"; transcript_name "mt-Rnr2-201"; 5 | chrM Mt_tRNA exon 2676 2750 . + . gene_id "ENSMUSG00000064340"; transcript_id "ENSMUST00000082391"; exon_number "1"; gene_name "mt-Tl1"; transcript_name "mt-Tl1-201"; 6 | chrM protein_coding exon 2751 3707 . + . gene_id "ENSMUSG00000064341"; transcript_id "ENSMUST00000082392"; exon_number "1"; gene_name "mt-Nd1"; transcript_name "mt-Nd1-201"; 7 | chrM protein_coding CDS 2751 3704 . + 0 gene_id "ENSMUSG00000064341"; transcript_id "ENSMUST00000082392"; exon_number "1"; gene_name "mt-Nd1"; transcript_name "mt-Nd1-201"; protein_id "ENSMUSP00000080991"; 8 | chrM protein_coding stop_codon 3705 3707 . + 0 gene_id "ENSMUSG00000064341"; transcript_id "ENSMUST00000082392"; exon_number "1"; gene_name "mt-Nd1"; transcript_name "mt-Nd1-201"; 9 | chrM Mt_tRNA exon 3706 3774 . + . gene_id "ENSMUSG00000064342"; transcript_id "ENSMUST00000082393"; exon_number "1"; gene_name "mt-Ti"; transcript_name "mt-Ti-201"; 10 | chrM Mt_tRNA exon 3772 3842 . - . gene_id "ENSMUSG00000064343"; transcript_id "ENSMUST00000082394"; exon_number "1"; gene_name "mt-Tq"; transcript_name "mt-Tq-201"; 11 | chrM Mt_tRNA exon 3845 3913 . + . gene_id "ENSMUSG00000064344"; transcript_id "ENSMUST00000082395"; exon_number "1"; gene_name "mt-Tm"; transcript_name "mt-Tm-201"; 12 | chrM protein_coding exon 3914 4951 . + . gene_id "ENSMUSG00000064345"; transcript_id "ENSMUST00000082396"; exon_number "1"; gene_name "mt-Nd2"; transcript_name "mt-Nd2-201"; 13 | chrM protein_coding CDS 3914 4948 . + 0 gene_id "ENSMUSG00000064345"; transcript_id "ENSMUST00000082396"; exon_number "1"; gene_name "mt-Nd2"; transcript_name "mt-Nd2-201"; protein_id "ENSMUSP00000080992"; 14 | chrM protein_coding stop_codon 4949 4951 . + 0 gene_id "ENSMUSG00000064345"; transcript_id "ENSMUST00000082396"; exon_number "1"; gene_name "mt-Nd2"; transcript_name "mt-Nd2-201"; 15 | chrM Mt_tRNA exon 4950 5016 . + . gene_id "ENSMUSG00000064346"; transcript_id "ENSMUST00000082397"; exon_number "1"; gene_name "mt-Tw"; transcript_name "mt-Tw-201"; 16 | chrM Mt_tRNA exon 5018 5086 . - . gene_id "ENSMUSG00000064347"; transcript_id "ENSMUST00000082398"; exon_number "1"; gene_name "mt-Ta"; transcript_name "mt-Ta-201"; 17 | chrM Mt_tRNA exon 5089 5159 . - . gene_id "ENSMUSG00000064348"; transcript_id "ENSMUST00000082399"; exon_number "1"; gene_name "mt-Tn"; transcript_name "mt-Tn-201"; 18 | chrM Mt_tRNA exon 5192 5257 . - . gene_id "ENSMUSG00000064349"; transcript_id "ENSMUST00000082400"; exon_number "1"; gene_name "mt-Tc"; transcript_name "mt-Tc-201"; 19 | chrM Mt_tRNA exon 5260 5326 . - . gene_id "ENSMUSG00000064350"; transcript_id "ENSMUST00000082401"; exon_number "1"; gene_name "mt-Ty"; transcript_name "mt-Ty-201"; 20 | chrM protein_coding exon 5328 6872 . + . gene_id "ENSMUSG00000064351"; transcript_id "ENSMUST00000082402"; exon_number "1"; gene_name "mt-Co1"; transcript_name "mt-Co1-201"; 21 | chrM protein_coding CDS 5328 6869 . + 0 gene_id "ENSMUSG00000064351"; transcript_id "ENSMUST00000082402"; exon_number "1"; gene_name "mt-Co1"; transcript_name "mt-Co1-201"; protein_id "ENSMUSP00000080993"; 22 | chrM protein_coding start_codon 5328 5330 . + 0 gene_id "ENSMUSG00000064351"; transcript_id "ENSMUST00000082402"; exon_number "1"; gene_name "mt-Co1"; transcript_name "mt-Co1-201"; 23 | chrM protein_coding stop_codon 6870 6872 . + 0 gene_id "ENSMUSG00000064351"; transcript_id "ENSMUST00000082402"; exon_number "1"; gene_name "mt-Co1"; transcript_name "mt-Co1-201"; 24 | chrM Mt_tRNA exon 6870 6938 . - . gene_id "ENSMUSG00000064352"; transcript_id "ENSMUST00000082403"; exon_number "1"; gene_name "mt-Ts1"; transcript_name "mt-Ts1-201"; 25 | chrM Mt_tRNA exon 6942 7011 . + . gene_id "ENSMUSG00000064353"; transcript_id "ENSMUST00000082404"; exon_number "1"; gene_name "mt-Td"; transcript_name "mt-Td-201"; 26 | chrM protein_coding exon 7013 7696 . + . gene_id "ENSMUSG00000064354"; transcript_id "ENSMUST00000082405"; exon_number "1"; gene_name "mt-Co2"; transcript_name "mt-Co2-201"; 27 | chrM protein_coding CDS 7013 7693 . + 0 gene_id "ENSMUSG00000064354"; transcript_id "ENSMUST00000082405"; exon_number "1"; gene_name "mt-Co2"; transcript_name "mt-Co2-201"; protein_id "ENSMUSP00000080994"; 28 | chrM protein_coding start_codon 7013 7015 . + 0 gene_id "ENSMUSG00000064354"; transcript_id "ENSMUST00000082405"; exon_number "1"; gene_name "mt-Co2"; transcript_name "mt-Co2-201"; 29 | chrM protein_coding stop_codon 7694 7696 . + 0 gene_id "ENSMUSG00000064354"; transcript_id "ENSMUST00000082405"; exon_number "1"; gene_name "mt-Co2"; transcript_name "mt-Co2-201"; 30 | chrM Mt_tRNA exon 7700 7764 . + . gene_id "ENSMUSG00000064355"; transcript_id "ENSMUST00000082406"; exon_number "1"; gene_name "mt-Tk"; transcript_name "mt-Tk-201"; 31 | chrM protein_coding exon 7766 7969 . + . gene_id "ENSMUSG00000064356"; transcript_id "ENSMUST00000082407"; exon_number "1"; gene_name "mt-Atp8"; transcript_name "mt-Atp8-201"; 32 | chrM protein_coding CDS 7766 7966 . + 0 gene_id "ENSMUSG00000064356"; transcript_id "ENSMUST00000082407"; exon_number "1"; gene_name "mt-Atp8"; transcript_name "mt-Atp8-201"; protein_id "ENSMUSP00000080995"; 33 | chrM protein_coding start_codon 7766 7768 . + 0 gene_id "ENSMUSG00000064356"; transcript_id "ENSMUST00000082407"; exon_number "1"; gene_name "mt-Atp8"; transcript_name "mt-Atp8-201"; 34 | chrM protein_coding stop_codon 7967 7969 . + 0 gene_id "ENSMUSG00000064356"; transcript_id "ENSMUST00000082407"; exon_number "1"; gene_name "mt-Atp8"; transcript_name "mt-Atp8-201"; 35 | chrM protein_coding exon 7927 8607 . + . gene_id "ENSMUSG00000064357"; transcript_id "ENSMUST00000082408"; exon_number "1"; gene_name "mt-Atp6"; transcript_name "mt-Atp6-201"; 36 | chrM protein_coding CDS 7927 8604 . + 0 gene_id "ENSMUSG00000064357"; transcript_id "ENSMUST00000082408"; exon_number "1"; gene_name "mt-Atp6"; transcript_name "mt-Atp6-201"; protein_id "ENSMUSP00000080996"; 37 | chrM protein_coding start_codon 7927 7929 . + 0 gene_id "ENSMUSG00000064357"; transcript_id "ENSMUST00000082408"; exon_number "1"; gene_name "mt-Atp6"; transcript_name "mt-Atp6-201"; 38 | chrM protein_coding stop_codon 8605 8607 . + 0 gene_id "ENSMUSG00000064357"; transcript_id "ENSMUST00000082408"; exon_number "1"; gene_name "mt-Atp6"; transcript_name "mt-Atp6-201"; 39 | chrM protein_coding exon 8607 9390 . + . gene_id "ENSMUSG00000064358"; transcript_id "ENSMUST00000082409"; exon_number "1"; gene_name "mt-Co3"; transcript_name "mt-Co3-201"; 40 | chrM protein_coding CDS 8607 9390 . + 0 gene_id "ENSMUSG00000064358"; transcript_id "ENSMUST00000082409"; exon_number "1"; gene_name "mt-Co3"; transcript_name "mt-Co3-201"; protein_id "ENSMUSP00000080997"; 41 | chrM protein_coding start_codon 8607 8609 . + 0 gene_id "ENSMUSG00000064358"; transcript_id "ENSMUST00000082409"; exon_number "1"; gene_name "mt-Co3"; transcript_name "mt-Co3-201"; 42 | chrM Mt_tRNA exon 9391 9458 . + . gene_id "ENSMUSG00000064359"; transcript_id "ENSMUST00000082410"; exon_number "1"; gene_name "mt-Tg"; transcript_name "mt-Tg-201"; 43 | chrM protein_coding exon 9459 9806 . + . gene_id "ENSMUSG00000064360"; transcript_id "ENSMUST00000082411"; exon_number "1"; gene_name "mt-Nd3"; transcript_name "mt-Nd3-201"; 44 | chrM protein_coding CDS 9459 9803 . + 0 gene_id "ENSMUSG00000064360"; transcript_id "ENSMUST00000082411"; exon_number "1"; gene_name "mt-Nd3"; transcript_name "mt-Nd3-201"; protein_id "ENSMUSP00000080998"; 45 | chrM protein_coding stop_codon 9804 9806 . + 0 gene_id "ENSMUSG00000064360"; transcript_id "ENSMUST00000082411"; exon_number "1"; gene_name "mt-Nd3"; transcript_name "mt-Nd3-201"; 46 | chrM Mt_tRNA exon 9808 9875 . + . gene_id "ENSMUSG00000064361"; transcript_id "ENSMUST00000082412"; exon_number "1"; gene_name "mt-Tr"; transcript_name "mt-Tr-201"; 47 | chrM protein_coding exon 9877 10173 . + . gene_id "ENSMUSG00000065947"; transcript_id "ENSMUST00000084013"; exon_number "1"; gene_name "mt-Nd4l"; transcript_name "mt-Nd4l-201"; 48 | chrM protein_coding CDS 9877 10170 . + 0 gene_id "ENSMUSG00000065947"; transcript_id "ENSMUST00000084013"; exon_number "1"; gene_name "mt-Nd4l"; transcript_name "mt-Nd4l-201"; protein_id "ENSMUSP00000081021"; 49 | chrM protein_coding start_codon 9877 9879 . + 0 gene_id "ENSMUSG00000065947"; transcript_id "ENSMUST00000084013"; exon_number "1"; gene_name "mt-Nd4l"; transcript_name "mt-Nd4l-201"; 50 | chrM protein_coding stop_codon 10171 10173 . + 0 gene_id "ENSMUSG00000065947"; transcript_id "ENSMUST00000084013"; exon_number "1"; gene_name "mt-Nd4l"; transcript_name "mt-Nd4l-201"; 51 | chrM protein_coding exon 10167 11544 . + . gene_id "ENSMUSG00000064363"; transcript_id "ENSMUST00000082414"; exon_number "1"; gene_name "mt-Nd4"; transcript_name "mt-Nd4-201"; 52 | chrM protein_coding CDS 10167 11544 . + 0 gene_id "ENSMUSG00000064363"; transcript_id "ENSMUST00000082414"; exon_number "1"; gene_name "mt-Nd4"; transcript_name "mt-Nd4-201"; protein_id "ENSMUSP00000081000"; 53 | chrM protein_coding start_codon 10167 10169 . + 0 gene_id "ENSMUSG00000064363"; transcript_id "ENSMUST00000082414"; exon_number "1"; gene_name "mt-Nd4"; transcript_name "mt-Nd4-201"; 54 | chrM Mt_tRNA exon 11546 11612 . + . gene_id "ENSMUSG00000064364"; transcript_id "ENSMUST00000082415"; exon_number "1"; gene_name "mt-Th"; transcript_name "mt-Th-201"; 55 | chrM Mt_tRNA exon 11613 11671 . + . gene_id "ENSMUSG00000064365"; transcript_id "ENSMUST00000082416"; exon_number "1"; gene_name "mt-Ts2"; transcript_name "mt-Ts2-201"; 56 | chrM Mt_tRNA exon 11671 11741 . + . gene_id "ENSMUSG00000064366"; transcript_id "ENSMUST00000082417"; exon_number "1"; gene_name "mt-Tl2"; transcript_name "mt-Tl2-201"; 57 | chrM protein_coding exon 11742 13565 . + . gene_id "ENSMUSG00000064367"; transcript_id "ENSMUST00000082418"; exon_number "1"; gene_name "mt-Nd5"; transcript_name "mt-Nd5-201"; 58 | chrM protein_coding CDS 11742 13562 . + 0 gene_id "ENSMUSG00000064367"; transcript_id "ENSMUST00000082418"; exon_number "1"; gene_name "mt-Nd5"; transcript_name "mt-Nd5-201"; protein_id "ENSMUSP00000081001"; 59 | chrM protein_coding stop_codon 13563 13565 . + 0 gene_id "ENSMUSG00000064367"; transcript_id "ENSMUST00000082418"; exon_number "1"; gene_name "mt-Nd5"; transcript_name "mt-Nd5-201"; 60 | chrM protein_coding exon 13552 14070 . - . gene_id "ENSMUSG00000064368"; transcript_id "ENSMUST00000082419"; exon_number "1"; gene_name "mt-Nd6"; transcript_name "mt-Nd6-201"; 61 | chrM protein_coding CDS 13555 14070 . - 0 gene_id "ENSMUSG00000064368"; transcript_id "ENSMUST00000082419"; exon_number "1"; gene_name "mt-Nd6"; transcript_name "mt-Nd6-201"; protein_id "ENSMUSP00000081002"; 62 | chrM protein_coding start_codon 14068 14070 . - 0 gene_id "ENSMUSG00000064368"; transcript_id "ENSMUST00000082419"; exon_number "1"; gene_name "mt-Nd6"; transcript_name "mt-Nd6-201"; 63 | chrM protein_coding stop_codon 13552 13554 . - 0 gene_id "ENSMUSG00000064368"; transcript_id "ENSMUST00000082419"; exon_number "1"; gene_name "mt-Nd6"; transcript_name "mt-Nd6-201"; 64 | chrM Mt_tRNA exon 14071 14139 . - . gene_id "ENSMUSG00000064369"; transcript_id "ENSMUST00000082420"; exon_number "1"; gene_name "mt-Te"; transcript_name "mt-Te-201"; 65 | chrM protein_coding exon 14145 15288 . + . gene_id "ENSMUSG00000064370"; transcript_id "ENSMUST00000082421"; exon_number "1"; gene_name "mt-Cytb"; transcript_name "mt-Cytb-201"; 66 | chrM protein_coding CDS 14145 15288 . + 0 gene_id "ENSMUSG00000064370"; transcript_id "ENSMUST00000082421"; exon_number "1"; gene_name "mt-Cytb"; transcript_name "mt-Cytb-201"; protein_id "ENSMUSP00000081003"; 67 | chrM protein_coding start_codon 14145 14147 . + 0 gene_id "ENSMUSG00000064370"; transcript_id "ENSMUST00000082421"; exon_number "1"; gene_name "mt-Cytb"; transcript_name "mt-Cytb-201"; 68 | chrM Mt_tRNA exon 15289 15355 . + . gene_id "ENSMUSG00000064371"; transcript_id "ENSMUST00000082422"; exon_number "1"; gene_name "mt-Tt"; transcript_name "mt-Tt-201"; 69 | chrM Mt_tRNA exon 15356 15422 . - . gene_id "ENSMUSG00000064372"; transcript_id "ENSMUST00000082423"; exon_number "1"; gene_name "mt-Tp"; transcript_name "mt-Tp-201"; 70 | chrM miRNA exon 16115 16209 . - . gene_id "ENSMUSG00000076442"; transcript_id "ENSMUST00000103243"; exon_number "1"; gene_name "mmu-mir-805"; transcript_name "mmu-mir-805.1-201"; 71 | -------------------------------------------------------------------------------- /genomes/Mmusculus/mm9/rnaseq/ref-transcripts.refFlat: -------------------------------------------------------------------------------- 1 | ENSMUST00000082387 ENSMUST00000082387 chrM + 0 68 68 68 1 0, 68, 2 | ENSMUST00000082388 ENSMUST00000082388 chrM + 69 1024 1024 1024 1 69, 1024, 3 | ENSMUST00000082389 ENSMUST00000082389 chrM + 1024 1093 1093 1093 1 1024, 1093, 4 | ENSMUST00000082390 ENSMUST00000082390 chrM + 1093 2675 2675 2675 1 1093, 2675, 5 | ENSMUST00000082391 ENSMUST00000082391 chrM + 2675 2750 2750 2750 1 2675, 2750, 6 | ENSMUST00000082392 ENSMUST00000082392 chrM + 2750 3707 2750 3707 1 2750, 3707, 7 | ENSMUST00000082393 ENSMUST00000082393 chrM + 3705 3774 3774 3774 1 3705, 3774, 8 | ENSMUST00000082394 ENSMUST00000082394 chrM - 3771 3842 3842 3842 1 3771, 3842, 9 | ENSMUST00000082395 ENSMUST00000082395 chrM + 3844 3913 3913 3913 1 3844, 3913, 10 | ENSMUST00000082396 ENSMUST00000082396 chrM + 3913 4951 3913 4951 1 3913, 4951, 11 | ENSMUST00000082397 ENSMUST00000082397 chrM + 4949 5016 5016 5016 1 4949, 5016, 12 | ENSMUST00000082398 ENSMUST00000082398 chrM - 5017 5086 5086 5086 1 5017, 5086, 13 | ENSMUST00000082399 ENSMUST00000082399 chrM - 5088 5159 5159 5159 1 5088, 5159, 14 | ENSMUST00000082400 ENSMUST00000082400 chrM - 5191 5257 5257 5257 1 5191, 5257, 15 | ENSMUST00000082401 ENSMUST00000082401 chrM - 5259 5326 5326 5326 1 5259, 5326, 16 | ENSMUST00000082402 ENSMUST00000082402 chrM + 5327 6872 5327 6872 1 5327, 6872, 17 | ENSMUST00000082403 ENSMUST00000082403 chrM - 6869 6938 6938 6938 1 6869, 6938, 18 | ENSMUST00000082404 ENSMUST00000082404 chrM + 6941 7011 7011 7011 1 6941, 7011, 19 | ENSMUST00000082405 ENSMUST00000082405 chrM + 7012 7696 7012 7696 1 7012, 7696, 20 | ENSMUST00000082406 ENSMUST00000082406 chrM + 7699 7764 7764 7764 1 7699, 7764, 21 | ENSMUST00000082407 ENSMUST00000082407 chrM + 7765 7969 7765 7969 1 7765, 7969, 22 | ENSMUST00000082408 ENSMUST00000082408 chrM + 7926 8607 7926 8607 1 7926, 8607, 23 | ENSMUST00000082409 ENSMUST00000082409 chrM + 8606 9390 8606 9390 1 8606, 9390, 24 | ENSMUST00000082410 ENSMUST00000082410 chrM + 9390 9458 9458 9458 1 9390, 9458, 25 | ENSMUST00000082411 ENSMUST00000082411 chrM + 9458 9806 9458 9806 1 9458, 9806, 26 | ENSMUST00000082412 ENSMUST00000082412 chrM + 9807 9875 9875 9875 1 9807, 9875, 27 | ENSMUST00000084013 ENSMUST00000084013 chrM + 9876 10173 9876 10173 1 9876, 10173, 28 | ENSMUST00000082414 ENSMUST00000082414 chrM + 10166 11544 10166 11544 1 10166, 11544, 29 | ENSMUST00000082415 ENSMUST00000082415 chrM + 11545 11612 11612 11612 1 11545, 11612, 30 | ENSMUST00000082416 ENSMUST00000082416 chrM + 11612 11671 11671 11671 1 11612, 11671, 31 | ENSMUST00000082417 ENSMUST00000082417 chrM + 11670 11741 11741 11741 1 11670, 11741, 32 | ENSMUST00000082418 ENSMUST00000082418 chrM + 11741 13565 11741 13565 1 11741, 13565, 33 | ENSMUST00000082419 ENSMUST00000082419 chrM - 13551 14070 13551 14070 1 13551, 14070, 34 | ENSMUST00000082420 ENSMUST00000082420 chrM - 14070 14139 14139 14139 1 14070, 14139, 35 | ENSMUST00000082421 ENSMUST00000082421 chrM + 14144 15288 14144 15288 1 14144, 15288, 36 | ENSMUST00000082422 ENSMUST00000082422 chrM + 15288 15355 15355 15355 1 15288, 15355, 37 | ENSMUST00000082423 ENSMUST00000082423 chrM - 15355 15422 15422 15422 1 15355, 15422, 38 | ENSMUST00000103243 ENSMUST00000103243 chrM - 16114 16209 16209 16209 1 16114, 16209, 39 | -------------------------------------------------------------------------------- /genomes/Mmusculus/mm9/seq/mm9-resources.yaml: -------------------------------------------------------------------------------- 1 | version: 1 2 | 3 | aliases: 4 | snpeff: NCBIM37 5 | ensembl: mouse 6 | 7 | rnaseq: 8 | transcripts: ../rnaseq/ref-transcripts.gtf 9 | transcripts_mask: ../rnaseq/ref-transcripts-mask.gtf -------------------------------------------------------------------------------- /genomes/Mmusculus/mm9/seq/mm9.dict: -------------------------------------------------------------------------------- 1 | @HD VN:1.0 SO:unsorted 2 | @SQ SN:chrM LN:16299 UR:file:/home/bchapman/bio/bcbb/nextgen/tests/data/automated/tool-data/../../genomes/mm9/seq/mm9.fa M5:11c8af2a2528b25f2c080ab7da42edda 3 | -------------------------------------------------------------------------------- /genomes/Mmusculus/mm9/seq/mm9.fa.fai: -------------------------------------------------------------------------------- 1 | chrM 16299 6 50 51 2 | -------------------------------------------------------------------------------- /rnaseq/Hsapiens/stranded/README.md: -------------------------------------------------------------------------------- 1 | These are from human tumors, using a paired-end, strand-specific dUTP (fr-firstrand) library preparation protocol. Reads are 100 BP in length. 2 | -------------------------------------------------------------------------------- /rnaseq/Hsapiens/stranded/test_1.fq.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/roryk/tiny-test-data/4dc37f0aaf5b2f3eec260a91689effa4197bd2a3/rnaseq/Hsapiens/stranded/test_1.fq.gz -------------------------------------------------------------------------------- /rnaseq/Hsapiens/stranded/test_2.fq.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/roryk/tiny-test-data/4dc37f0aaf5b2f3eec260a91689effa4197bd2a3/rnaseq/Hsapiens/stranded/test_2.fq.gz -------------------------------------------------------------------------------- /rnaseq/Hsapiens/unstranded/Hsapiens_1.fq.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/roryk/tiny-test-data/4dc37f0aaf5b2f3eec260a91689effa4197bd2a3/rnaseq/Hsapiens/unstranded/Hsapiens_1.fq.gz -------------------------------------------------------------------------------- /rnaseq/Hsapiens/unstranded/Hsapiens_2.fq.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/roryk/tiny-test-data/4dc37f0aaf5b2f3eec260a91689effa4197bd2a3/rnaseq/Hsapiens/unstranded/Hsapiens_2.fq.gz -------------------------------------------------------------------------------- /rnaseq/Hsapiens/unstranded/README: -------------------------------------------------------------------------------- 1 | These are paired-end, 35 bp RNA-seq reads of the Sanger quality. They were taken from reads mapping to MT. 2 | -------------------------------------------------------------------------------- /rnaseq/Mmusculus/unstranded/Mmusculus_1.fq.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/roryk/tiny-test-data/4dc37f0aaf5b2f3eec260a91689effa4197bd2a3/rnaseq/Mmusculus/unstranded/Mmusculus_1.fq.gz -------------------------------------------------------------------------------- /rnaseq/Mmusculus/unstranded/Mmusculus_2.fq.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/roryk/tiny-test-data/4dc37f0aaf5b2f3eec260a91689effa4197bd2a3/rnaseq/Mmusculus/unstranded/Mmusculus_2.fq.gz -------------------------------------------------------------------------------- /rnaseq/Mmusculus/unstranded/README: -------------------------------------------------------------------------------- 1 | These are paired-end, 35 bp RNA-seq reads of the Sanger quality. They were taken from reads mapping to MT. 2 | -------------------------------------------------------------------------------- /rnaseq/Mmusculus/unstranded/align/Test1-ready.bai: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/roryk/tiny-test-data/4dc37f0aaf5b2f3eec260a91689effa4197bd2a3/rnaseq/Mmusculus/unstranded/align/Test1-ready.bai -------------------------------------------------------------------------------- /rnaseq/Mmusculus/unstranded/align/Test1-ready.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/roryk/tiny-test-data/4dc37f0aaf5b2f3eec260a91689effa4197bd2a3/rnaseq/Mmusculus/unstranded/align/Test1-ready.bam -------------------------------------------------------------------------------- /scripts/fastq_clip.py: -------------------------------------------------------------------------------- 1 | from argparse import ArgumentParser 2 | import sys 3 | from itertools import ifilter 4 | 5 | from Bio import SeqIO 6 | 7 | QUALITY_CONVERSION_TYPES = ["fastq-sanger", "fastq-solexa", "fastq-illumina"] 8 | 9 | def is_long_enough(read_length): 10 | def too_small(record): 11 | return len(str(record.seq)) > read_length 12 | return too_small 13 | 14 | def trim_records(records, read_length): 15 | for record in records: 16 | yield record[0:read_length] 17 | 18 | def main(in_file, in_format, read_length): 19 | 20 | with open(in_file, "r") as in_handle: 21 | parser = SeqIO.parse(in_handle, in_format) 22 | too_small = ifilter(is_long_enough(read_length), parser) 23 | SeqIO.write(trim_records(too_small, read_length), sys.stdout, in_format) 24 | 25 | if __name__ == "__main__": 26 | parser = ArgumentParser(description="simple script for converting " 27 | "fastq quality scores.") 28 | parser.add_argument("--read-length", type=int, help="Length to clip reads to.") 29 | parser.add_argument("--in-format", help="Quality format of fastq-file.", 30 | default="fastq-sanger", 31 | choices=QUALITY_CONVERSION_TYPES) 32 | parser.add_argument("in_file", help="FASTQ file to clip.") 33 | args = parser.parse_args() 34 | main(args.in_file, args.in_format, args.read_length) 35 | -------------------------------------------------------------------------------- /scripts/fastq_convert.py: -------------------------------------------------------------------------------- 1 | from argparse import ArgumentParser 2 | import sys 3 | 4 | from Bio import SeqIO 5 | 6 | QUALITY_CONVERSION_TYPES = ["fastq-sanger", "fastq-solexa", "fastq-illumina"] 7 | 8 | def main(in_file, in_format, out_format): 9 | with open(in_file, "r") as in_handle: 10 | SeqIO.convert(in_handle, in_format, sys.stdout, out_format) 11 | 12 | if __name__ == "__main__": 13 | parser = ArgumentParser(description="simple script for converting " 14 | "fastq quality scores.") 15 | parser.add_argument("--in-format", help="Quality format to convert from.", 16 | choices=QUALITY_CONVERSION_TYPES) 17 | parser.add_argument("--out-format", help="Quality format to convert to.", 18 | choices=QUALITY_CONVERSION_TYPES) 19 | parser.add_argument("in_file", help="FASTQ file to convert.") 20 | args = parser.parse_args() 21 | main(args.in_file, args.in_format, args.out_format) 22 | -------------------------------------------------------------------------------- /vcf/README.md: -------------------------------------------------------------------------------- 1 | Tiny variant call format files extracted from samtools [VCF v4.3 specification](samtools.github.io/hts-specs/VCFv4.3.pdf). Also cancer-related VCFs [from bcbio's `./run_tests.sh cancermulti`](http://bcbio-nextgen.readthedocs.io/en/latest/contents/pipelines.html#cancer-variant-calling) and its resulting {S1 & S2}-variants.vcf files under the `data` directory. 2 | -------------------------------------------------------------------------------- /vcf/sample1-bcbio-cancer.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##FILTER= 3 | ##FORMAT= 4 | ##FORMAT= 5 | ##FORMAT= 6 | ##FORMAT= 7 | ##FORMAT= 8 | ##GATKCommandLine= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##INFO= 14 | ##INFO= 15 | ##INFO= 16 | ##INFO= 17 | ##INFO= 18 | ##INFO= 19 | ##INFO= 20 | ##INFO= 21 | ##INFO= 22 | ##INFO= 23 | ##INFO= 24 | ##INFO= 25 | ##INFO= 26 | ##INFO= 27 | ##INFO= 28 | ##INFO= 29 | ##INFO= 30 | ##INFO= 31 | ##INFO= 32 | ##contig= 33 | ##contig= 34 | ##reference=file:///home/chapmanb/bio/bcbio-nextgen/tests/data/automated/tool-data/../../genomes/hg19/seq/hg19.fa 35 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT S1 36 | chrM 150 . T C 7470.77 . AC=2;AF=1.00;AN=2;DP=244;Dels=0.00;FS=0.000;GC=46.00;HRun=1;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=30.62 GT:AD:DP:GQ:PL 1/1:0,244:244:99:7499,722,0 37 | chrM 152 rs117135796 T C 8577.77 . AC=2;AF=1.00;AN=2;DB;DP=250;Dels=0.00;FS=0.000;GC=46.02;HRun=1;HaplotypeScore=0.8667;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=34.31 GT:AD:DP:GQ:PL 1/1:0,250:250:99:8606,737,0 38 | chrM 195 . C TGG 7551.77 . AC=2;AF=1.00;AN=2;DP=250;Dels=0.00;FS=0.000;GC=45.57;HRun=1;HaplotypeScore=1.9810;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=30.21 GT:AD:DP:GQ:PL 1/1:0,250:250:99:7580,710,0 39 | chrM 410 . A T 7375.77 . AC=2;AF=1.00;AN=2;DP=250;Dels=0.00;FS=0.000;GC=45.64;HRun=3;HaplotypeScore=1.7323;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=29.50 GT:AD:DP:GQ:PL 1/1:0,250:250:99:7404,710,0 40 | chrM 2261 . C T 7152.77 . AC=2;AF=1.00;AN=2;DP=250;Dels=0.00;FS=0.000;GC=39.15;HRun=0;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=28.61 GT:AD:DP:GQ:PL 1/1:0,250:250:99:7181,730,0 41 | chrM 2354 . C T 7216.77 . AC=2;AF=1.00;AN=2;DP=250;Dels=0.00;FS=0.000;GC=41.15;HRun=1;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=28.87 GT:AD:DP:GQ:PL 1/1:0,250:250:99:7245,736,0 42 | chrM 2485 . C T 5493.77 . AC=2;AF=1.00;AN=2;DP=250;Dels=0.00;FS=0.000;GC=43.14;HRun=0;HaplotypeScore=1.9258;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=21.98 GT:AD:DP:GQ:PL 1/1:13,237:238:99:5522,553,0 43 | chrM 2708 . G A 4890.77 . AC=2;AF=1.00;AN=2;DP=218;Dels=0.00;FS=0.000;GC=46.88;HRun=1;HaplotypeScore=0.9973;MLEAC=2;MLEAF=1.00;MQ=59.97;MQ0=0;QD=22.43 GT:AD:DP:GQ:PL 1/1:0,218:218:99:4919,505,0 44 | chrM 3493 . A C 358.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-8.442;DP=250;Dels=0.00;FS=231.833;GC=50.37;HRun=3;HaplotypeScore=15.2879;MLEAC=1;MLEAF=0.500;MQ=59.88;MQ0=0;MQRankSum=1.168;QD=1.44;ReadPosRankSum=-2.352 GT:AD:DP:GQ:PL 0/1:153,97:238:99:387,0,3449 45 | chrM 4746 . A G 7554.77 . AC=2;AF=1.00;AN=2;DP=250;Dels=0.00;FS=0.000;GC=41.15;HRun=0;HaplotypeScore=1.8255;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=30.22 GT:AD:DP:GQ:PL 1/1:0,250:250:99:7583,728,0 46 | chr22 150 . T C 7470.77 . AC=2;AF=1.00;AN=2;DP=244;Dels=0.00;FS=0.000;GC=46.00;HRun=1;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=30.62 GT:AD:DP:GQ:PL 1/1:0,244:244:99:7499,722,0 47 | chr22 153 . T TCC 7470.77 . AC=2;AF=1.00;AN=2;DP=244;Dels=0.00;FS=0.000;GC=46.00;HRun=1;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=30.62 GT:AD:DP:GQ:PL 1/1:0,244:244:99:7499,722,0 48 | -------------------------------------------------------------------------------- /vcf/sample2-bcbio-cancer.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##FILTER= 3 | ##FORMAT= 4 | ##FORMAT= 5 | ##FORMAT= 6 | ##FORMAT= 7 | ##FORMAT= 8 | ##GATKCommandLine= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##INFO= 14 | ##INFO= 15 | ##INFO= 16 | ##INFO= 17 | ##INFO= 18 | ##INFO= 19 | ##INFO= 20 | ##INFO= 21 | ##INFO= 22 | ##INFO= 23 | ##INFO= 24 | ##INFO= 25 | ##INFO= 26 | ##INFO= 27 | ##INFO= 28 | ##contig= 29 | ##contig= 30 | ##reference=file:///home/chapmanb/bio/bcbio-nextgen/tests/data/automated/tool-data/../../genomes/hg19/seq/hg19.fa 31 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT S2 32 | chrM 150 . T C 15303.77 . AC=2;AF=1.00;AN=2;DP=338;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=28.65 GT:AD:GQ:PL 1/1:0,337:99:15332,1044,0 33 | chrM 152 rs117135796 T C 15303.77 . AC=2;AF=1.00;AN=2;DB;DP=341;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=33.43 GT:AD:GQ:PL 1/1:0,340:99:15332,1044,0 34 | chrM 410 . A T 3324.77 . AC=2;AF=1.00;AN=2;DP=129;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=25.77 GT:AD:GQ:PL 1/1:0,129:99:3353,387,0 35 | chrM 2261 . C T 6856.77 . AC=2;AF=1.00;AN=2;DP=283;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=24.23 GT:AD:GQ:PL 1/1:0,283:99:6885,847,0 36 | chrM 2354 . C T 7126.77 . AC=2;AF=1.00;AN=2;DP=293;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=24.32 GT:AD:GQ:PL 1/1:0,293:99:7155,877,0 37 | chrM 2485 . C T 7200.77 . AC=2;AF=1.00;AN=2;DP=271;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=26.57 GT:AD:GQ:PL 1/1:0,271:99:7229,820,0 38 | chrM 2708 . G A 1185.77 . AC=2;AF=1.00;AN=2;DP=49;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=24.20 GT:AD:GQ:PL 1/1:0,49:99:1214,147,0 39 | chrM 3493 . A C 34.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-6.882;DP=138;FS=169.468;MLEAC=1;MLEAF=0.500;MQ=59.88;MQ0=0;MQRankSum=1.076;QD=0.25;ReadPosRankSum=-3.296 GT:AD:GQ:PL 0/1:107,31:63:63,0,2418 40 | chrM 4746 . A G 6290.77 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.502;DP=245;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;MQRankSum=0.488;QD=25.68;ReadPosRankSum=-0.587 GT:AD:GQ:PL 1/1:1,244:99:6319,714,0 41 | chr22 150 . T C 15303.77 . AC=2;AF=1.00;AN=2;DP=338;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=28.65 GT:AD:GQ:PL 0/1:0,337:99:15332,1044,0 42 | -------------------------------------------------------------------------------- /vcf/spec-svs-v4.1.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.1 2 | ##fileDate=20100501 3 | ##reference=1000GenomesPilot-NCBI36 4 | ##assembly=ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/release/sv/breakpoint_assemblies.fasta 5 | ##INFO= 6 | ##INFO= 7 | ##INFO= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##ALT= 14 | ##ALT= 15 | ##ALT= 16 | ##ALT= 17 | ##ALT= 18 | ##ALT= 19 | ##ALT= 20 | ##ALT= 21 | ##ALT= 22 | ##ALT= 23 | ##FORMAT= 24 | ##FORMAT= 25 | ##FORMAT= 26 | ##FORMAT= 27 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 28 | 1 2827694 rs2376870 CGTGGATGCGGGGAC C . PASS SVTYPE=DEL;END=2827708;HOMLEN=1;HOMSEQ=G;SVLEN=-14 GT:GQ 1/1:13.9 29 | 2 321682 . T 6 PASS SVTYPE=DEL;END=321887;SVLEN=-205;CIPOS=-56,20;CIEND=-10,62 GT:GQ 0/1:12 30 | 2 14477084 . C 12 PASS SVTYPE=DEL;END=14477381;SVLEN=-297;CIPOS=-22,18;CIEND=-12,32 GT:GQ 0/1:12 31 | 3 9425916 . C 23 PASS SVTYPE=INS;END=9425916;SVLEN=6027;CIPOS=-16,22 GT:GQ 1/1:15 32 | 3 12665100 . A 14 PASS SVTYPE=DUP;END=12686200;SVLEN=21100;CIPOS=-500,500;CIEND=-500,500 GT:GQ:CN:CNQ ./.:0:3:16.2 33 | 4 18665128 . T 11 PASS SVTYPE=DUP;END=18665204;SVLEN=76;CIPOS=-10,10;CIEND=-10,10 GT:GQ:CN:CNQ ./.:0:5:8.3 34 | -------------------------------------------------------------------------------- /vcf/spec-v4.3.vcf: -------------------------------------------------------------------------------- 1 | ##fileformat=VCFv4.3 2 | ##fileDate=20090805 3 | ##source=myImputationProgramV3.1 4 | ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta 5 | ##contig= 6 | ##phasing=partial 7 | ##INFO= 8 | ##INFO= 9 | ##INFO= 10 | ##INFO= 11 | ##INFO= 12 | ##INFO= 13 | ##FILTER= 14 | ##FILTER= 15 | ##FORMAT= 16 | ##FORMAT= 17 | ##FORMAT= 18 | ##FORMAT= 19 | #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 20 | 20 14370 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,. 21 | 20 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3 22 | 20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4 23 | 20 1230237 . T . 47 PASS NS=3;DP=13;AA=T GT:GQ:DP:HQ 0|0:54:7:56,60 0|0:48:4:51,51 0/0:61:2 24 | 20 1234567 microsat1 GTC G,GTCT 50 PASS NS=3;DP=9;AA=G GT:GQ:DP 0/1:35:4 0/2:17:2 1/1:40:3 25 | -------------------------------------------------------------------------------- /wgs/README.md: -------------------------------------------------------------------------------- 1 | # Mitocondrial reads from WGS 2 | 3 | The reads in `mt_1.fq.gz` and `mt_2.fq.gz` comes from the normal sample of the synthetic dataset 3 of the ICGC-TCGA DREAM challenge. Reads aligning to the mitochontrion were extracted from the aligned BAM file, and converted to fastq format. The dataset is 2x101 paired illumina reads, In total 4597 read pairs. Average coverage after removing duplicate is around 110x, but varies wildly. This provides suffcient depth to test variant calling downstream. 4 | -------------------------------------------------------------------------------- /wgs/mt.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/roryk/tiny-test-data/4dc37f0aaf5b2f3eec260a91689effa4197bd2a3/wgs/mt.bam -------------------------------------------------------------------------------- /wgs/mt.parquet.adam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/roryk/tiny-test-data/4dc37f0aaf5b2f3eec260a91689effa4197bd2a3/wgs/mt.parquet.adam -------------------------------------------------------------------------------- /wgs/mt.sorted.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/roryk/tiny-test-data/4dc37f0aaf5b2f3eec260a91689effa4197bd2a3/wgs/mt.sorted.bam -------------------------------------------------------------------------------- /wgs/mt.sorted.bam.bai: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/roryk/tiny-test-data/4dc37f0aaf5b2f3eec260a91689effa4197bd2a3/wgs/mt.sorted.bam.bai -------------------------------------------------------------------------------- /wgs/mt_1.fq.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/roryk/tiny-test-data/4dc37f0aaf5b2f3eec260a91689effa4197bd2a3/wgs/mt_1.fq.gz -------------------------------------------------------------------------------- /wgs/mt_2.fq.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/roryk/tiny-test-data/4dc37f0aaf5b2f3eec260a91689effa4197bd2a3/wgs/mt_2.fq.gz --------------------------------------------------------------------------------