How does Tophat balance read-mismatches with seqment-mismatches?

zshuhua · 10-24-2013, 08:00 AM

Hello,
I'm using Tophat v 2.05 to map 75 bases single end reads generated by Illumina Hi-seq2000. I set segment-length with 25 as default and want to maximum mismatches of 3 allowed for each read. May I set segment-mismatches with 3?
As my understanding, I can do that because Tophat manual has default value of 2 for read-mismatches and segment-mismatches respectively.
So in my case, Tophat will select the best aligned read allowed 3 mismatches by joining 3 segments with mismatches 3, 0,0 or 2,1,0 or 1,1,1. Am I right?
Thanks for your help in advance.

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10-24-2013, 08:00 AM	#1
zshuhua Junior Member Location: Ontario Join Date: May 2010 Posts: 4	How does Tophat balance read-mismatches with seqment-mismatches? Hello, I'm using Tophat v 2.05 to map 75 bases single end reads generated by Illumina Hi-seq2000. I set segment-length with 25 as default and want to maximum mismatches of 3 allowed for each read. May I set segment-mismatches with 3? As my understanding, I can do that because Tophat manual has default value of 2 for read-mismatches and segment-mismatches respectively. So in my case, Tophat will select the best aligned read allowed 3 mismatches by joining 3 segments with mismatches 3, 0,0 or 2,1,0 or 1,1,1. Am I right? Thanks for your help in advance.