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nofar 10-02-2014 04:02 AM

HTSeq - paired reads count
I was wondering if there were any changes in the latest version on HTSeq (after Version 0.5.4) that could affect the count of paired reads (other than what's mentioned in the documentation)?
I have a test dataset which I tested a few months ago (before the version update) and I see that the new version gives slightly different results (about 10% of the genes's counts have changed).
Based on the documentation, the only change that could possibly affect the counts is the default for parameter minaqual, but I ran the new version with a=0 (which was the default in the previous version) and there was still a difference in the counts. What else could be affecting this? I haven't changed anything in the dataset or in the parameters/versions of other programs (same version of tophat, same GTF file etc.)

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