Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
BWA:getting hits with given number of mismatches and indels Chandana Bioinformatics 0 01-11-2012 11:03 AM
bowtie paired end mismatches madsaan Bioinformatics 0 06-22-2011 09:26 AM
Bowtie: number of alignments Nick Bioinformatics 1 03-04-2011 11:58 AM
bowtie sam output, number of mismatches sridharacharya Bioinformatics 2 01-08-2011 06:22 PM
Bowtie mapping with more mismatches mapper Bioinformatics 0 01-05-2011 03:11 AM

Thread Tools
Old 05-08-2011, 01:55 AM   #1
Location: Israel

Join Date: Oct 2010
Posts: 37
Default Number of mismatches in Bowtie

Hi all,

Bowtie's manual says the following about -v mode:
"-v <int> Report alignments with at most <int> mismatches"

I understood from this that for paired end reads the whole alignment, including both ends, will contain up to <int> mismatches.

But when I ran my data with -v 2 mode I got the following MD:Z values for 2 ends of the same read:

and another example:

So it seems like 2 mismatches are allowed per end.

Just wanted to make sure that this what -v means, and that I didn't do something else that caused this.

Rachelly 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 07:08 AM.

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