how to adapt this for analysis of paired-end reads with different fragment lengths (ChIP, INPUT)

[ykumar22]

In my project, I need to analyse coverage of ChIP-seq signal from two ranges of fragment lengths. I bin reads into smallBin (30-150bp) and bigBin (150-300 bp). Relative proportion of reads in these bins has to be preserved in order to be of any use to my question.

What do you suggest I should do?

Thanks