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Old 04-29-2010, 12:51 PM   #1
Location: Barcelona, Spain

Join Date: Jun 2009
Posts: 36
Question splicing stats from Tophat's SAM output


I just want tocheck thifat this is the right way to do it.

Using Tophat output (accepted_hits.sam) calculate statistics about spliced vs non_spliced hits.

Spliced reads looks like this:
8_105_178_344 0 scaffold09041 94954 255 9M7543N41M * 0 0 CAGTTAATTTCTGCGAACCGAAGATAACAACAGTGATAAGGGTCGCTACTAA BABBBBBBABA@BBBBBB@<B@@4>@A@0<0:?37<=999.<9=4<?7%2 NM:i:0 XS:A:- NS:i:0

grab CIGAR string "9M7543N41M", anything with number before N larger than minimal intron size (50 by default) should be a spliced read.

Is this correct?

Darek Kedra
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