SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
How to extract multi-mapped reads by samtools? mavishou RNA Sequencing 5 12-05-2016 05:27 AM
bwa bug (?) leading to samtools segfault fpepin Bioinformatics 4 05-03-2011 10:49 AM
A samtools v0.1.11 bug??? nturay Bioinformatics 0 04-28-2011 02:52 AM
Asking for suggestiona on samtools bug fixing lh3 Bioinformatics 15 10-27-2010 02:34 PM
weird samtools pileup bug xiang Bioinformatics 4 01-29-2010 04:52 AM

Reply
 
Thread Tools
Old 12-22-2010, 09:33 PM   #1
xinwu
Member
 
Location: Beijing

Join Date: Jul 2010
Posts: 33
Default samtools flagstats bug or it does not support multi-reads?

Hi All,
I used bowtie to map reads with k = 10 (allow at most 10 alignments for one read). I hoped to get some statistical result for mapping but found the summary of bowtie result was not consistent with samtools flagstats. It seems that samtools flagstats and picard ONLY support sam file with ONE alignment. In fact, they can only work on ALIGNMENT rather than READ.
For example, I got ~25% reads mapped from bowtie log but ~56% from samtools flagstats and picard. Since one read may have multiple alignments, samtools and picard treat each alignment as a mapped read! The confusing thing is the label for the result claims it is calculated based on READ! For example, PCT_PF_READS_ALIGNED is used in picard, but it will mislead you, since its value is the percentage of number of valid alignments NOT reads themselves.
I do think this maybe a bug if the label claims as such?
Any answers or explanations? Thanks.
xinwu 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 04:23 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO