Science Score: 54.0%
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✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
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✓Academic publication links
Links to: zenodo.org -
○Academic email domains
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○Institutional organization owner
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○Scientific vocabulary similarity
Low similarity (8.6%) to scientific vocabulary
Repository
A Snakemake pipeline for RNASeq data analysis
Basic Info
Statistics
- Stars: 0
- Watchers: 0
- Forks: 0
- Open Issues: 0
- Releases: 3
Metadata Files
README.md
Snakemake workflow: RNASeq
A Snakemake-based pipeline for RNASeq data analysis.
Starting from fastq files, the pipeline merges files from different units and perform reads quality trimming.
The pseudoaligner kallisto is used to estimate transcripts abundance, with resulting .h5 files that can be imported into DESeq2for DE Analysis.
STAR 2-pass mapping is used for read alignment.
Quality Control is perfomed with FastQC and RSeQC and included in an interactive MultiQC report.
Authors
- Matteo Massidda, University of Sassari
- Vincenzo Rallo, Institute for Genetic and Biomedical Research (IRGB) - National Research Council (CNR)
Usage
The usage of this workflow is described in the Snakemake Workflow Catalog.
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).
INSTRUCTIONS
Create a virtual environment with the command:
commandline
mamba create -c bioconda -c conda-forge --name snakemake snakemake=7.18 snakedeploy
and activate it:
commandline
conda activate snakemake
You can perform the pipeline deploy defining a directory my_dest_dir for analysis output and a pipeline tag for a specific version:
bash
snakedeploy deploy-workflow https://github.com/GeneBANGS/RNASeq.git
my_desd_dir
--tag v1.1.0
To run the pipeline, go inside the deployed pipeline folder and use the command:
bash
snakemake --use-conda -p --cores all
Owner
- Name: GeneBANGS
- Login: GeneBANGS
- Kind: organization
- Repositories: 1
- Profile: https://github.com/GeneBANGS
Citation (CITATION.cff)
cff-version: 1.1.0
message: "If you use this software, please cite it as below."
authors:
- family-names: "Massidda"
given-names: "Matteo"
orcid: "https://orcid.org/0000-0002-5246-5585"
- family-names: "Rallo"
given-names: "Vincenzo"
orcid: "https://orcid.org/0000-0002-8938-5650"
title: "RNASeq: A Snakemake-based workflow for reproducible RNA-Seq data analysis"
version: v1.1.0
doi: 10.5281/zenodo.8369279
date-released: 2023-09-22