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  • GTF to TrascriptDB

    Hi !!

    I am trying to use the DESeq R package and it seems like I have to create an annotation TranscriptDB object . The problem is that I have to use my own annotation, and any other annotation from UCSC wont work for me and I can't figure out how to create such object from a GTF file that I've created...

    Thanks ahead!

  • #2
    I wrote a quick R script to turn a GTF (made by cufflinks) into a GenomicFeatures TranscriptDB object a few months ago - no guarantees but I hope it helps you out

    cuff 2 db. GitHub Gist: instantly share code, notes, and snippets.

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