A collection of snakemake pipelines for performing common analyses with RNA-seq data.
Each pipeline has: * a README * a conda recipe for dependencies * a test dataset * a snakemake script * parallel execution via a snakejob script
bazam-pipeline - convert BAMs to FASTQs as quickly as possible for a set of BAMs
RAPiD-tips - documentation on how to run the RAPiD pipeline
collate_samples - group together RSEM outputs by gene and transcript for a set of files processed by RAPiD, group together QC outputs into a single table
qSVA-pipeline - run qSVA to find RNA quality-associated surrogate variables (qSVs)
kallisto-pipeline - experimental workflows for generating custom kallisto indexes and running kallisto on lots of samples