Bug in featureCounts?

[brinda]

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.

[shi]

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.

As stated in the program usage and users guide, '-p' should only be used for paired-end reads. So don't use it for single end reads.

When '-M' is specified, reads with NH>1 will NOT be ignored. They will be counted. Again, please read the program usage and users guide.

Wei