Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
How many mismatches does Tophat allow? wudinger Bioinformatics 2 10-17-2014 04:54 PM
How to allow more mismatches in BWA? Karenj Bioinformatics 15 01-17-2013 07:26 AM
Ambiguous bases vs mismatches in Tophat ameyer Bioinformatics 0 10-01-2012 10:59 AM
Tophat with --initial-read-mismatches command Error: chenyao Bioinformatics 6 08-24-2011 11:17 PM
Concentration of mismatches close to read ends in "Whole Transcriptome" protocol hingamp SOLiD 42 05-27-2010 05:43 AM

Thread Tools
Old 10-24-2013, 08:00 AM   #1
Junior Member
Location: Ontario

Join Date: May 2010
Posts: 4
Default How does Tophat balance read-mismatches with seqment-mismatches?

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.
zshuhua is offline   Reply With Quote

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 02:24 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO