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README.md

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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.