Questions: counting reads mapped to exon-intron boundaries?

[SeqMlife]

Hi, everyone,

Needs some help here. I'm new in RNAseq. Just wondering is there a quick way to count how many reads have mapped to the exon-intron boundaries?
I have sorted bam file, exon bed file, intron bed file.
Thanks!

[swbarnes2]

Try BEDTools IntersectBed to get reads that overlap your exon boundaries, but not completely.

[SeqMlife]

Try BEDTools IntersectBed to get reads that overlap your exon boundaries, but not completely.

Thanks!
I will give it a try

[aggp11]

Try BEDTools IntersectBed to get reads that overlap your exon boundaries, but not completely.

Hi,

Would this mean that we create a BED file which has the start and end coordinates as the "END" of the previous exon and the "Start" of the next? Also, could you explain the incomplete overlap as well?

Thank you!