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RNA-pipelines

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

Contents

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