I have some tissue RNA-SEQ samples and I have mapped it to hg19 ref genome to get the bam files. I am trying to get the exon counts for a particular exon for all those tissue samples from the bam files. This exon is not annotated in the gif/gff file. I have the coordinates of this exon and have made an exon.bed file which just has one entry which is my exon coordinate. I am trying to use various methods to get exon count for this exon, but they don't seem to give me accurate results.
I will explain a bit about the exon. My exon is considered to be a micro exon and therefore the read splits into more than one place. Sometimes this exon is completely skipped and hence we have alternative isoform.
When I try to use multiBamCov, I am getting those reads also counted which is skipping this micro exon completely. This is because the upstream 5' ss is the same for this micro exon and other exon down stream. I want to count those reads which are
contained within the exon some part of the read overlaps with the exon as well as all those splice junctions count which include this exon
How can I do this. Hope to hear soon.