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Old 07-05-2012, 12:09 PM   #3
pbluescript
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Location: Boston

Join Date: Nov 2009
Posts: 224
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It would be nice if there was a tool that could take a bam file aligned to a transcriptome and along with a gtf file convert the transcriptome coordinates to genome coordinates.

I have asked if such a tool exists here before and done my own searching with no luck. I've cobbled together a solution to the problem, but it's not fast and it only works in my specific case.
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