https://github.com/saketkc/rna-seq-snakemake

Snakemake based pipeline for RNA-Seq analysis
https://github.com/saketkc/rna-seq-snakemake

bioinformatics pipeline rna-seq-analysis rna-seq-snakemake snakemake

Last synced: about 4 hours ago
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Snakemake based pipeline for RNA-Seq analysis

• Host: GitHub
• URL: https://github.com/saketkc/rna-seq-snakemake
• Owner: saketkc
• License: bsd-2-clause
• Created: 2016-11-07T10:13:57.000Z (about 8 years ago)
• Default Branch: master
• Last Pushed: 2019-06-26T19:04:00.000Z (over 5 years ago)
• Last Synced: 2024-11-01T02:51:48.967Z (7 days ago)
• Topics: bioinformatics, pipeline, rna-seq-analysis, rna-seq-snakemake, snakemake
• Language: R
• Size: 54.7 KB
• Stars: 31
• Watchers: 4
• Forks: 12
• Open Issues: 1
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# 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](Snakefile_fastq_multilane.snake) - For multilane paired end fastq files

2. [Snakefile_sra_pe](Snakefile_sra_pe) - For paired end `*.sra` files

3. [Snakefile_sra_se](Snakefile_sra_se) - For single end `*.sra` files

4. [Snakefile_fastq](Snakefile_fastq) - For paired end fastq files

## Dependecies

- snakemake

- STAR

- bamtools

- DESeq2

- qualimap

- multiqc

- rseqc