├── Assignments └── README.md ├── Day-1 ├── bash │ ├── 1.intro.md │ ├── 2.dirStructure_and_pipes.md │ ├── 3.variables_conditional_and_loops.md │ ├── 4.string_and_arithmatics.md │ ├── 5.automation.md │ ├── 6.regular_expression.md │ ├── README.md │ ├── assets │ │ ├── 1.png │ │ ├── 2.png │ │ ├── 3.png │ │ ├── 4.png │ │ ├── 5.png │ │ ├── 6.png │ │ ├── 7.png │ │ ├── 8.png │ │ └── regex1.png │ └── dataFiles_tutorial_gtf2bed.md └── regex_cheat_sheet.pdf ├── Day-2 ├── FASTQC_tutorial.md ├── Fastq_exploration.md ├── Trimmomatic_tutorial.md ├── hairpin.fa.gz └── seqkit_examples.md ├── Day-3 ├── git-tutorial.md ├── git │ ├── README.md │ └── resources │ │ └── github-git-cheat-sheet.pdf ├── pseudobam-GTF.png ├── sample_data │ ├── dog_chr5.fa.gz │ ├── gencode.v29.annotation.gtf.gz │ └── gencode.v29.pc_transcripts.fa.gz └── seq_alignment.md ├── Day-4 ├── hisat_stringtie.md ├── trinity.md └── trinity_assessement.md ├── Day-5 ├── functional-annotation.md ├── functional-annotation_createDB.md └── gtf-compare.md ├── Day-6 ├── advanced │ ├── DE.R │ └── main.sh ├── deseq1.r ├── dif_exp.md └── draw-heatmap.r ├── LICENSE ├── README.md └── sample_data ├── SP1.fq ├── hairpin.fa.gz ├── lamina.bed ├── octane.pdb └── pentane.pdb /Assignments/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/drtamermansour/nu-ngs01/HEAD/Assignments/README.md -------------------------------------------------------------------------------- /Day-1/bash/1.intro.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/drtamermansour/nu-ngs01/HEAD/Day-1/bash/1.intro.md -------------------------------------------------------------------------------- /Day-1/bash/2.dirStructure_and_pipes.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/drtamermansour/nu-ngs01/HEAD/Day-1/bash/2.dirStructure_and_pipes.md 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