I'm not sure that was the question that was asked. I think that output is from TopHat/Cufflinks, and the question is really "How do I tally the output of TopHat/Cufflinks to identify the transcription start sites associated with the identified isoforms?". Happy to be shown otherwise however ;)
Transcription Start Site For Each Isoform
This is follow up to a question I just asked and which was nicely responded by a colleague in the forum. For a given gene I happen to have 3 different test IDs, all assigned to the same nearest reference ID. TCONS00002453 j NM001002901 XLOC000914 TCONS00002454 j NM001002901 XLOC000914 TCONS00002455 = NM001002901 XLOC_000914
I additionally have 2 tss IDs for this particular gene TSS1509 XLOC000914 TSS1510 XLOC000914
The question is: how do I go about finding the actual start site that distinguishes each isoform?
Thanks, G.
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Anthony Mathelier
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GPR
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GPR
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You can retrieve all human transcripts information, including TSS positions, from the mySQL database at UCSC using something like:
mysql -h genome-mysql.cse.ucsc.edu -A -u genome -D hg19 -e 'select name, name2, chrom, txStart, txEnd, strand from refGene\G'
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Anthony Mathelier
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Anthony Mathelier
OK. Sorry having misunderstood the question. I remove my answer right now.
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Anthony Mathelier
Thanks for attempting to answer my question. I now realize that it wasn't well formulated. My confusion really originated from trying to come to terms with the outputs given by cummeRbund, igv and the isoform tracking file. All confusing for a begginer, it narrowed down to some isoforms tagged class_code J in the tracking file.
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