We are using featureCounts for both and single-end and pair-end data. In the command we always have the '-p' flag on, assuming it will be ignored for single-end data. However, we notice that the function of '-M' is affected because of '-p' flag.
When we run single-end data with '-M' flag, all the reads with NH > 1 are ignored, as expected. However, when we run single-end data with both '-M' and '-p' flag, the multi-mapping reads (NH > 1) are no longer ignored.
The '-p' should have an effect on filtering multi-mapping reads. I'm attaching a sample sam and gtf file where this may be observed.
When we run single-end data with '-M' flag, all the reads with NH > 1 are ignored, as expected. However, when we run single-end data with both '-M' and '-p' flag, the multi-mapping reads (NH > 1) are no longer ignored.
The '-p' should have an effect on filtering multi-mapping reads. I'm attaching a sample sam and gtf file where this may be observed.
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