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Old 06-01-2011, 08:49 PM   #2
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Location: Rockville, MD

Join Date: Jan 2009
Posts: 126

Hi Avinash,

In both of the runs, if I compare the results with the actual known transcripts from Ensembl, it seems like I am missing many known junctions.
For any one tissue type, a certain (possibly substantial) fraction of the known junctions will not be present simply due to tissue-specific expression of different isoforms. As such, I wouldn't worry about this part of your question.

Also, given the Genomic coordinates of a splice junction, is there a way I can extract, from the Tophat output, the no of IUM (Initially Unmapped reads) that Tophat mapped to span that particular junction?
I doubt this is possible, unless you are MUCH better than hacking into the code and the tmp files than I am.

Best of luck,

shurjo is offline   Reply With Quote