GTF to TrascriptDB

moriah

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Join Date: Dec 2010

Posts: 23
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#1

GTF to TrascriptDB

08-28-2011, 10:42 PM

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!
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frozenlyse

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Join Date: Sep 2008

Posts: 135
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#2

08-29-2011, 01:23 AM

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

https://gist.github.com/1178072

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