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rna-seq-salmon-deseq2

Snakemake workflow for RNA-Seq differential transcript analysis using Salmon/Deseq2

https://github.com/niekwit/rna-seq-salmon-deseq2

Science Score: 49.0%

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    CITATION.cff file
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    Found 3 DOI reference(s) in README
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    Links to: zenodo.org
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    Low similarity (9.6%) to scientific vocabulary

Keywords

bioinformatics snakemake snakemake-workflow
Last synced: 6 months ago · JSON representation

Repository

Snakemake workflow for RNA-Seq differential transcript analysis using Salmon/Deseq2

Basic Info
  • Host: GitHub
  • Owner: niekwit
  • License: mit
  • Language: Python
  • Default Branch: main
  • Homepage:
  • Size: 317 MB
Statistics
  • Stars: 5
  • Watchers: 1
  • Forks: 1
  • Open Issues: 1
  • Releases: 5
Topics
bioinformatics snakemake snakemake-workflow
Created over 2 years ago · Last pushed 10 months ago
Metadata Files
Readme License Citation

README.md

Snakemake workflow: rna-seq-salmon-deseq2

Snakemake Tests DOI

A Snakemake workflow for wicked-fast paired-end RNA-seq analysis with Salmon and DESeq2.

If you use this workflow in a paper, don't forget to give credits to the authors by citing the URL of this (original) repository and its DOI (see above).

Software dependencies

Usage

Preparing data and code

Create a main analysis directory with the subdirectories config/, reads/, and workflow/.

Place all your paired-end fastq files files in the reads folder. These should have the extensions R1001.fastq.gz/R2001.fastq.gz for read 1 and read2, respectively.

The config/ directory should contain two files: config.yml and samples.csv.

Meta information of the samples are described in samples.csv:

|sample|genotype |treatment |reference |batch | |------|-----------|-----------|----------|-------| |Control1|WT|Normoxia|yes|1| |Control2|WT|Normoxia|yes|1| |ControlHypoxia1|WT|Hypoxia|no|1| |ControlHypoxia2|WT|Hypoxia|no|1|

[!IMPORTANT] The sample names should correspond to the files name, eg. Control1R1001.fastq.gz and Control1R2001.fastqz for sample Control_1.

Analysis settings and resource

yaml genome: human # human or mouse gencode_genome_build: 44 fdr_cutoff: 0.05 # adj p value cut off for volcano plots fc_cutoff: 0.5 # log2 fold change cut off for volcano plots salmon-quant: extra_params: "" # additional arguments to pass to Salmon salmon-index: extra_params: "--gencode" deseq2: # custom model for DESeq2 design: "" resources: # computing resources trim: cpu: 8 time: 60 fastqc: cpu: 4 time: 60 mapping: cpu: 8 time: 120 deseq2: cpu: 6 time: 60 plotting: cpu: 2 time: 20

Owner

  • Name: Niek Wit
  • Login: niekwit
  • Kind: user
  • Location: Cambridge, UK
  • Company: University of Cambridge

Bioinformatician @ University of Cambridge working in the labs of Prof. James Nathan and Prof. Paul Lehner

GitHub Events

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Last Year
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Top Authors
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  • niekwit (1)
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Dependencies

.github/workflows/conventional-prs.yml actions
  • amannn/action-semantic-pull-request v3.4.0 composite
.github/workflows/main.yml actions
  • actions/checkout v2 composite
  • github/super-linter v4 composite
  • snakemake/snakemake-github-action v1.24.0 composite
.github/workflows/release-please.yml actions
  • GoogleCloudPlatform/release-please-action v2 composite
.docker/v0.7.0/Dockerfile docker
  • condaforge/mambaforge latest build
.docker/v0.7.1/Dockerfile docker
  • condaforge/mambaforge latest build
.docker/v0.7.2/Dockerfile docker
  • condaforge/miniforge3 latest build