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 1 month 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 (over 8 years ago)
- Default Branch: master
- Last Pushed: 2019-06-26T19:04:00.000Z (almost 6 years ago)
- Last Synced: 2025-03-27T22:12:41.402Z (about 2 months ago)
- Topics: bioinformatics, pipeline, rna-seq-analysis, rna-seq-snakemake, snakemake
- Language: R
- Size: 54.7 KB
- Stars: 31
- Watchers: 3
- 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