Not quite RNA-seq but trying to use same software

[egunth]

Hi there,

I have created a list of genomic loci that have enrichment between two samples experimentally and I want to create a list of FPKM values for these regions using ChIP-seq data. I tried writing a script to do this on my own but it's woefully slow for the amount of data I need to handle. Two questions: First, is this a valid approach? I'm just trying to treat these enriched regions as "transcripts" and use FPKM as a way to quantify their abundance across different ChIP-seq samples. The two ideas seem analogous (mRNA level vs ChIP enrichment) so this seemed like the best way to do that. Second, what software can I use to calculate FPKM for this custom list of regions using a SAM, BAM, or BED file of reads?

Thanks in advance,
Eric

[dpryan]

Have you looked into just using DiffBind?