Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
bwa alignment failed CTGF Bioinformatics 1 10-24-2011 12:35 AM
BWA alignment followed by TopHat slny Bioinformatics 9 06-06-2011 06:19 AM
Spliced alignment with BWA telos SOLiD 7 10-06-2010 06:32 AM
Alignment statistics from bwa? menenuh Bioinformatics 1 01-29-2010 01:14 PM
BWA Alignment Errors Seq1234 Bioinformatics 0 12-15-2009 08:59 PM

Thread Tools
Old 07-05-2011, 12:59 PM   #1
Location: 86001

Join Date: Aug 2010
Posts: 21
Default BWA: Is alignment summary available?

Is there a tool associated with BWA that can provide a concise overall summary of the alignments/pairing, such as:
1. How many reads did not map?
2. How many single ends mapped?
3. How many reads were successfully paired
Protaeus is offline   Reply With Quote
Old 07-05-2011, 01:47 PM   #2
Senior Member
Location: San Diego

Join Date: May 2008
Posts: 912

I don't think so. I use samtools flagstat.
swbarnes2 is offline   Reply With Quote
Old 07-05-2011, 06:12 PM   #3
Senior Member
Location: East Coast, US

Join Date: Jun 2010
Posts: 177

I use picard
DZhang 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 12:23 AM.

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