So i am working on rna seq data. I am using gsnap for my analysis(though i have also used tophat). With tophat , a junctions.bed file is produced which actually tells us about the splicing patterns going on.
Using gsnap i am able to produce sam/bam files. Is there a way i can convert these sam/bam files into something similar to junctions.bed files.
My main goal is to see what is the difference between junctions produced from tophat and gsnap. Tophat produces junctions.bed file but gsnap doesnt. So is there a way i can get a junctions file from sam/bam output of gsnap.
Hope to hear from you guys soon