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Old 05-07-2018, 09:17 AM   #1
xrao
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Location: Houston USA

Join Date: Mar 2014
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Default featureCounts does not recognize BWA XA tag?

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
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