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Created by domingue@domingueMaintainer

dge workflow: add GTF an argument for differential gene expression

Relates to the DGE analysis and it would have two uses:

  1. retrieval of "accurate" gene lengths, exonic regions only, to calculate RPKM and FPM using DESeq2 in-built functionality (more details here)
  2. GTFs already contain a wealth of information which currently needs to be retrieved wiht biomaRt. Getting it from the GTF would make the process faster, more reproducible (in my experience biomaRt changes quite often) and it would work even for organisms not present in biomart or other marts (eg. planaria)
Edited by domingue