Bulk RNA-seq pipeline, release p1.1
phalaena:pipeline:PA-PL-transcriptomics-bulkseq
Bulk RNA-seq quantification on Illumina short-read transcriptomes. We trim with fastp, build a decoy-aware transcriptome index, quasi-map reads with Salmon, aggregate per-sample quants into a counts matrix, render plots and a MultiQC report, and emit a canonical summary.json matching phalaena_backend/pipelines/SUMMARY_SCHEMA.md; the assistant reads this contract directly. The pipeline is input-shape-agnostic: paired-end, single-end, or a mix of both in one submission (the pasilla validation slot runs two SE controls alongside two PE knockdowns). Differential expression is not computed inside the pipeline; the counts matrix is the contract handed to downstream DESeq2 / edgeR / limma-voom. Pipeline ID transcriptomics_bulkseq. Source: phalaena_backend/pipelines/2.1_transcriptomics_bulkseq/. API entry: phalaena_api/app/pipelines/transcriptomics_bulkseq.py.
- kind
- pipeline
- status
- draft
- github:phalaena-automata/monorepo/phalaena_backend/pipelines/2.1_transcriptomics_bulkseq
View Bulk RNA-seq pipeline, release p1.1 on the Phalaena Wiki