Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
BWA-MEM and X0/X1/etc flags mturchin20 Bioinformatics 5 07-15-2015 07:54 AM
BWA -mem FrankiB RNA Sequencing 2 02-07-2014 09:31 AM
BWA MEM question CHObot Bioinformatics 5 08-08-2013 04:04 AM
bwa mem segfault; bwa bwasw breaks MarkDuplicates ElenaN Bioinformatics 2 06-30-2013 11:23 PM
bwa mem -R option dakin Bioinformatics 2 05-02-2013 08:42 AM

Thread Tools
Old 02-24-2015, 06:38 AM   #1
Location: Hungary

Join Date: Feb 2012
Posts: 19
Smile BWA MEM question

Dear all,

I just have a question about bwa mem alignment. I ran the following simple command:

bwa mem <fa> <fastq> -t 5

Before the alignment I checked the number of reads with fastqc and then after alignment I counted the IDs present in the sam file with grep '<common ID> | wc -l and I got different results.
What causes the difference? Is the multi-mapper reads present in the sam file?

Total reads: 24 961 320
Aligned reads: 24 961 535

Thank you for the answere,
Liy is offline   Reply With Quote
Old 02-24-2015, 06:48 AM   #2
Senior Member
Location: Berlin, Germany

Join Date: Jan 2015
Posts: 137

samtools view -S -f 0x100 <file.sam>
to get the multimappers.

Last edited by sarvidsson; 02-24-2015 at 06:54 AM. Reason: too quick
sarvidsson 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 02:13 AM.

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