README.md

rna-seq-snakamake

Snakemake based pipeline for RNA-Seq analysis

Inputs to all snakefiles are specified using a config.py, and generally is as simple as specifiying the directory containing all *.fq/*.fq.gz/*.fastq.gz/*.sra files.

1. Snakefile_fastq_multilane.snake - For multilane paired end fastq files

2. Snakefile_sra_pe - For paired end *.sra files

3. Snakefile_sra_se - For single end *.sra files

4. Snakefile_fastq - For paired end fastq files

Dependecies

• snakemake
• STAR
• bamtools
• DESeq2
• qualimap
• multiqc
• rseqc