Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
samtools flagstat output nguyendofx Bioinformatics 23 01-22-2014 05:45 AM
samtools flagstat output manore Bioinformatics 11 07-24-2013 12:19 AM
Samtools flagstat - no duplicates? Orr Shomroni Bioinformatics 3 11-25-2011 01:46 AM
SAMtools flagstat output interpretation a2z@blr Bioinformatics 2 10-20-2011 02:23 PM
samtools flagstat bair Bioinformatics 3 05-28-2010 07:15 AM

Thread Tools
Old 09-26-2011, 04:55 AM   #1
Location: Cape Town, South Africa

Join Date: May 2010
Posts: 30
Default Samtools flagstat

Hi there,

I ran tophat a few months ago on our rna-seq dataset and made a table showing the mapping statistics from samtools flagstat.

There were some queries about the data recently, so I decided to make sure I have the latest versions of all software and re-ran the analysis to see if it would improve.

When I ran flagstat and compared it with our previous results, I found that the output format from flagstat had changed. I then ran the current version of flagstat on our previously generated bam files from an older version of tophat to compare results, and found very weird results. The numbers I got was not comparable with the results I found using a previous version of flagstat.

My question is now.. How do I compare the old dataset with the new dataset using flagstat? Is flagstat calculating things differently? How can I report to my colleagues whether the mapping have improved. This obviously also has an effect downstream when I'm using the new version of Cufflinks.

Any ideas will be appreciated!
Anelda is offline   Reply With Quote

flagstat, samtools, tophat, versions

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 02:37 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO