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