Checking whether the reads aligned to specific gene have the specific exon in BAM file

Question

[dh.han]

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.

[GouthamAtla]

By loading that file into IGV ?

[dh.han]

feels like there are far too many reads to check the exon in igv

Answer 1

[GouthamAtla]

One option is to get the subset of bam file mapping to that region:

samtools view -b in.bam "chr:1000-100000" > in.subset.bam and view in IGV.

Other option is to get exonic counts using featureCounts.