SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
maq output biocc Bioinformatics 1 11-16-2010 01:38 PM
Maq filtered output. tachion Bioinformatics 0 05-19-2010 01:10 PM
MAQ and Samtools output dnusol Bioinformatics 0 01-22-2010 03:29 AM
MAQ output format m_elena_bioinfo Bioinformatics 0 12-09-2009 01:35 AM
MAQ output format seq_GA Bioinformatics 0 05-20-2009 11:43 PM

Reply
 
Thread Tools
Old 08-12-2010, 08:16 AM   #1
Ms@New
Member
 
Location: california

Join Date: Jun 2010
Posts: 17
Default maq output

Hi,

I want to have a distribution of number of mismatches in mapped reads from .map file. (how many of mapped reads have 1 mismatch, how may have 2, etc.)

it's a straight forward question, I'm guessing there is a a straight forward answer.
I found pileup and mapcheck, but none of them gives me the information that I need.

can any one help me with this?

Thanks
Ms@New is offline   Reply With Quote
Old 08-12-2010, 01:35 PM   #2
adamdeluca
Member
 
Location: Iowa City, IA

Join Date: Jul 2010
Posts: 95
Default

mapview gives you the number of mismatches for each read (column 10 I believe)
then:
cut -f10 | sort | uniq -c
adamdeluca is offline   Reply With Quote
Old 08-16-2010, 01:45 PM   #3
Ms@New
Member
 
Location: california

Join Date: Jun 2010
Posts: 17
Default

thanks adam
Ms@New is offline   Reply With Quote
Reply

Tags
maq output mismatch

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 06:47 PM.


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