This repo contains three example codebases.

1. GSE129011 is a workflow that was run on Savio cluster to compare the MPIPK strain to the Golor4 MGH1 strain reference using MPIPK RNAseq GSE129011.
2. softclip is a workflow that looks at regions where mapped reads are soft clipped.
3. TEtrimmer_partial contains some codes that are part of a complete software tool. I selected some codes here and I am the primary author of these codes.