How to calculate Exon-Intron junction perbase coverage?

Question

[PK]

Hi all,

I want to extract the Exon-Intron junction reads from the paired end RNA-Seq data. I’m only considering the reads that are crossing Exon-Intron boundary. For that I constructed a bed file flanking 100 nt up and downstream of the Exon-Intron junction. But I wanted to make sure that I have enough reads are supporting the junction. So I wanted to count the per-base frequency for the junctions. I’m considering only if I have >5x coverage. How can i calculate the per-base frequency? Is there any flaws in my strategy. if yes, please fell free to address.

Thanks.