GTF to TrascriptDB

[moriah]

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!

[frozenlyse]

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

https://gist.github.com/1178072