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Old 09-26-2011, 03:55 AM   #1
Anelda
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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!
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