├── DRUMMER.py ├── LICENSE ├── README.md ├── TESTDATA ├── Ad5.complete.transcript.chr.txt ├── Ad5.complete.transcripts.txt ├── Ad5.sample.single.trancripts.txt ├── Ad5.sample.transcripts.txt ├── Ad5_v9.1_complete.fasta ├── Ad5_v9.1_complete.fasta.fai ├── Adenovirus-Ad5.fasta ├── Adenovirus-Ad5.fasta.fai ├── Hsapiens.sample.fasta ├── Hsapiens.sample.transcripts.txt ├── exome.Ad5.MOD.bam ├── exome.Ad5.MOD.bam.bai ├── exome.Ad5.UNMOD.bam ├── exome.Ad5.UNMOD.bam.bai ├── isoform.Ad5.MOD.bam ├── isoform.Ad5.MOD.bam.bai ├── isoform.Ad5.MOD.depth.bam ├── isoform.Ad5.UNMOD.bam ├── isoform.Ad5.UNMOD.bam.bai ├── isoform.Hsapiens.MOD.sorted.bam ├── isoform.Hsapiens.MOD.sorted.bam.bai ├── isoform.Hsapiens.UNMOD.sorted.bam ├── isoform.Hsapiens.UNMOD.sorted.bam.bai ├── isoform2.Ad5.MOD.bam ├── isoform2.Ad5.MOD.bam.bai ├── isoform2.Ad5.UNMOD.bam ├── isoform2.Ad5.UNMOD.bam.bai ├── test_human.txt └── transcripts.old.txt ├── core ├── drummer-core-exome.sh └── drummer-core-isoform.sh ├── environment-setup.yml ├── extras ├── example_w_names.pdf ├── example_w_names_w_interval.pdf ├── individual_output_headers.txt ├── m6a_summary_plot.py ├── multi_plot.py └── summary.py └── modules ├── .DS_Store ├── DRUMMER-parse.py ├── Gtest.py ├── __pycache__ ├── Gtest.cpython-38.pyc ├── candidates.cpython-37.pyc ├── candidates.cpython-38.pyc ├── genomic.cpython-37.pyc ├── genomic.cpython-38.pyc ├── gtest.cpython-37.pyc ├── gtest.cpython-38.pyc ├── m6a_summary.cpython-37.pyc ├── m6a_summary.cpython-38.pyc ├── merge.cpython-37.pyc ├── merge.cpython-38.pyc ├── motif.cpython-37.pyc ├── motif.cpython-38.pyc ├── multiple_combine.cpython-37.pyc ├── multiple_combine.cpython-38.pyc ├── odds.cpython-37.pyc ├── odds.cpython-38.pyc ├── parsing_check.cpython-37.pyc ├── parsing_check.cpython-38.pyc ├── plot_multi.cpython-37.pyc ├── plot_multi.cpython-38.pyc ├── summary.cpython-37.pyc ├── summary.cpython-38.pyc ├── support.cpython-37.pyc ├── support.cpython-38.pyc ├── test_exome.cpython-37.pyc ├── 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