When running FeatureCounts with -R (report reads) the output bam file reads are tagged with XS, XN and XT.

I have bam files aligned with HISAT2 which writes the XS tag to store positive and negative strand (+,-).

Therefore each read line in the output bam file contains 2 XS tags and subsequent downstream software such as SAMTOOLS view -d tag filtering fails to correctly filter by XS tag. Is it possible to modify the FeatureCounts XS tag to another tag ID?

Thanks in advance, Chris

No, featureCounts cannot change the XS tag to a different tag, because that would change the information in the output. featureCounts needs to write correct assignment information as specified in the documentation.

I don't have any experience with a conflict with HISAT, so I can't suggest any solution to that, and I'm not very familiar with the report reads facility in general. This might not be the solution you want, but you could switch to the Subread aligner, which doesn't have the same conflict.