BulkIsoform
This github repo contains a pipeline for processing raw reads from paired end bulk RNA-seq data and extracting both gene level expression data and isoform level data using various tools, as well as some basic QC information. In addition, it contains the code for an R package to make loading and performing downstream analysis of this data easier. For details of both the pipeline and the package see the README files in their associated directories.
This is a companion discussion topic for the original entry at github.com/seanken/BulkIsoform/BulkPipeline