I've got a set of 100 bam files from a public experiment, I want to have an idea of splicing in each of them regarding three exons,without entering in some kind of depth-level procedure like Cufflinks or DEXSeq,
Lets say that my exons are named 1,2 and 3, and I want to know in how many samples I have a splicing event of the number two, so i was looking in the threads and I found that using coverageBed with my bed file of the three exons I could get some kind of idea per bam file
coverageBed -split -abam my_alignment -b exons_to.bed
Am I correct?
I was also thinking of getting the reads mapped in flanking end positions of read 1 and start of read 3 with samtools
What do you think about it? Any idea will be kindly appreciated
Thanks in advance!