Hi guys. So I did a cellranger count on my sample with my own new gene in the gtf annotation file.

And from the bam file I found some of the reads aligned to the gene according to its GX tag.

This gene however must have the specific exon sequence expressed, so I want to double check whether these aligned reads do have this specific exon sequence.

Right now I managed to use samtools to select the reads with the GX:gene tag from the bam file. How can I check whether these reads have that specific exonic sequence?

Thanks a lot! Appreciate any help.