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Old 10-29-2010, 09:35 AM   #3
Location: Ithaca

Join Date: Jan 2009
Posts: 26

Thank you Daehwan.

Before map reads to genome using tophat, contamination has already been cleaned. So I use fasta as input of tophat. And then I use bowtie map forward and reverse seqs to genome, the results are same.

After check the cigar field of sam file, I think you are right. All the different parts of forward and reverse results are unmapped reads. When I set the parameter -a to 4, the different parts of results are reduced.
Originally Posted by Daehwan View Post
Regarding each 50,000 seq difference between the results A and B, TopHat divides unmapped reads into several segments to find novel junctions, and a set of segments from the original reads can be different from that of segments from the reverse-complemented reads depending on the read length and the segment length, rendering different set of putative junctions.
And I will try the new version of tophat. Thanks again
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