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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!
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!