PacBio Long-read RNA-seq data processing pipeline

The following pipelines snakefile and snakefile_pigeon were designed and developed to process probe-enriched PacBio long-read RNA-seq data.

• snakefile contains the upstream part of the analysis.
• snakefile_pigeon contains the downstream part of the analysis.

This pipeline is also compatible with bulk RNA-seq PacBio long-read data.

Note these Snakemake pipelines make use of conda environments. .yaml environment files are also included in this repository. However, prior to use, switch prefix: YOUR_PATH placeholder with your conda path.