Hi all,
I have aligned my long 454 reads to the reference genome by using GMAP, a spliced read aligner. Now I want to extract the best set of intronic regions (gaps) in the alignments. Is there any tool could generate such information from a SAM file?
I feel this task is somewhat similar with indel calling, if you considered intron regions as huge deletions. But I'm not sure whether I can use indel calling tools to fit my need.
A simple (and naive) way I can image is counting the coverage of the gaps. The chromosome regions with many gaps mapped should be reliable intronic regions. For this purpose, is there a convenient way to calculate the coverage of gaps from a SAM file?
Thanks a lot,
Shuli
I have aligned my long 454 reads to the reference genome by using GMAP, a spliced read aligner. Now I want to extract the best set of intronic regions (gaps) in the alignments. Is there any tool could generate such information from a SAM file?
I feel this task is somewhat similar with indel calling, if you considered intron regions as huge deletions. But I'm not sure whether I can use indel calling tools to fit my need.
A simple (and naive) way I can image is counting the coverage of the gaps. The chromosome regions with many gaps mapped should be reliable intronic regions. For this purpose, is there a convenient way to calculate the coverage of gaps from a SAM file?
Thanks a lot,
Shuli
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