Snakemake based pipeline for RNA-Seq analysis
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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