Hello,
I am using featureCounts option -M. In the user guide, it says if it is specified, multi-mapping reads will be counted. The program uses the ‘NH’ tag to find multi-mapping reads. But I used BWA for mapping small microRNA reads. I found that featureCounts does not recognize BWA XA tag for identifying multi-mapping reads. Am I right? Do I have to just change the aligner?
Thank you very much for any help!
Thanks,
XY
I am using featureCounts option -M. In the user guide, it says if it is specified, multi-mapping reads will be counted. The program uses the ‘NH’ tag to find multi-mapping reads. But I used BWA for mapping small microRNA reads. I found that featureCounts does not recognize BWA XA tag for identifying multi-mapping reads. Am I right? Do I have to just change the aligner?
Thank you very much for any help!
Thanks,
XY