rnaseq_pipeline - v1.2.2 - minor fix

Full Changelog: https://github.com/epigen/rnaseq_pipeline/compare/v1.2.1...v1.2.2

- Python
Published by sreichl 8 months ago

rnaseq_pipeline - v1.2.1 - Small improvements

Full Changelog: https://github.com/epigen/rnaseq_pipeline/compare/v1.2.0...v1.2.1

- Python
Published by sreichl 8 months ago

rnaseq_pipeline - v1.2.0 - visualize sample annotations including QC metrics (interactively)

Full Changelog: https://github.com/epigen/rnaseq_pipeline/compare/v1.1.1...v1.2.0

- Python
Published by sreichl 8 months ago

rnaseq_pipeline - v1.1.1 - minor fix

Full Changelog: https://github.com/epigen/rnaseq_pipeline/compare/v1.1.0...v1.1.1

- Python
Published by sreichl 8 months ago

rnaseq_pipeline - v1.1.0 - minor improvements

Features * Exon-based gene annotation without BioMart using Biostars gene-annotation script (https://www.biostars.org/p/91218) * STAR aligner defaults set to ENCODE recommendations in config * Sample-annotation sanitization for R compatibility

Documentation * QC guideline enhancements in README (updated thresholds & descriptions)

Comprehensive testing * Sequencing modes: single-end & paired-end * Species: mouse & human * Sample sources: primary tissues & cell lines * Library protocols: Smart-seq2 (unstranded), NEBNext Ultra (unstranded), Quant-seq (stranded) * Cell types: Structural (epithelial, fibroblast, endothelial), Hematopoietic (13 cell types), CAR-T cells, sorted primary immune subsets, neurons

Full Changelog: https://github.com/epigen/rnaseq_pipeline/compare/v1.0.0...v1.1.0

- Python
Published by sreichl 9 months ago

rnaseq_pipeline - v1.0.0 - first stable version with complete docs

Features

• Provides an end-to-end Snakemake workflow for RNA-seq analysis, from unmapped BAM (uBAM) files to gene counts and annotations.
• Performs adapter/quality trimming using fastp.
• Aligns reads and quantifies gene expression using STAR (--quantMode GeneCounts), handling various library strandedness types.
• Generates a gene-by-sample count matrix (counts.csv).
• Retrieves gene annotations (ID, symbol, biotype, description) from Ensembl using biomaRt.
• Calculates exon-based GC content and cumulative exon length for each gene, suitable for downstream bias correction (e.g., with CQN).
• Creates gene (gene_annotation.csv) and sample (sample_annotation.csv) annotation files ready for downstream analysis.
• Integrates QC metrics from fastp, STAR, and RSeQC into a comprehensive MultiQC report.
• Designed as a compatible MrBiomics module.
• Includes input validation for read types specified in annotation vs. BAM file flags.
• Uses data streaming and temporary files for improved efficiency and reduced disk usage.
• Manages software dependencies using Conda environments.

Documentation & Usage

• Includes a README.md with workflow overview, features, usage instructions, QC guidelines, and a template Methods section.
• Provides a CITATION.cff file for standardized citation.
• Configuration is handled via config.yaml and annotation.csv, with explanations in config/README.md.
• Example configuration and annotation files are included.
• Exports Conda environment specifications (envs/*.yaml) used in the run for reproducibility.

We gratefully acknowledges adaptations from the snakemake-workflows/rna-seq-star-deseq2 workflow.

Full Changelog: https://github.com/epigen/rnaseq_pipeline/commits/v1.0.0

- Python
Published by sreichl 11 months ago