SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Alignment program that allows the greatest number of mismatches CarlHSLee Bioinformatics 3 02-25-2013 09:03 AM
BWA:getting hits with given number of mismatches and indels Chandana Bioinformatics 0 01-11-2012 10:03 AM
Number of mismatches in Bowtie Rachelly Bioinformatics 0 05-08-2011 12:55 AM
bowtie sam output, number of mismatches sridharacharya Bioinformatics 2 01-08-2011 05:22 PM
PubMed: A ChIP-seq defined genome-wide map of vitamin D receptor binding: Association Newsbot! Literature Watch 0 08-26-2010 02:00 AM

Reply
 
Thread Tools
Old 10-16-2015, 06:04 PM   #1
Pol8
Member
 
Location: USA

Join Date: Aug 2014
Posts: 33
Default map with defined number of mismatches

Hi,

how can I map reads against the reference genome, so that I'm sure they align continuously, but allowing from 0 to 5 mismatches in the alignment?
Or alternatively find in the alignment, reads that map with 0 to 5 mismatches?
Pol8 is offline   Reply With Quote
Old 10-16-2015, 08:20 PM   #2
Brian Bushnell
Super Moderator
 
Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,707
Default

BBMap has a "subfilter" flag - e.g. "subfilter=5" - which will ban alignments with more than 5 mismatches. It's a global aligner, so the reads will align continuously.
Brian Bushnell is offline   Reply With Quote
Reply

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 09:26 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO