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Old 11-08-2013, 01:41 AM   #6
feralBiologist
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Quote:
Originally Posted by rboettcher View Post
I agree with feralBiologist, but would switch to featureCounts instead of HTSeq-count for performance reasons (can be run multithreaded and does not require resorted SAM file).
Thanks for this suggestion. Have you checked whether HTSeq-count and featureCounts produce the same results? HTSeq-count supports certain counting models. Basically, the main issue is how to count reads that hit overlapping genes. I chose HTSeq-count because it is written by the author of DESeq and in the above paper has been "approved" also by the authors of edgeR. If featureCounts produces the same results than the switch would be painless but if there are differences than you need to look into the details.

EDIT: I realised that featureCounts is written by the authors of edgeR so it shall be straight-forward to substitute HTSeq-count. Thanks again to rboettcher.

Last edited by feralBiologist; 11-08-2013 at 01:56 AM.
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