Hi all,

I recently have some Gro-seq data. What I want to do is this:

1. Workflow

Counting how many reads per 200bp windows per chromosome. For this, my work flow is as followed:
fasq -> fasq groomer -> bowtie -> BAM to SAM -> interval
BED -> 200 bp windows
regional variation -> feature

2. Questions: how do I sort and save per chromosome? For example, I would like to compare X chromosome versus autosomes or X versus chromosome 1?

Please accept my appreciation,

Di Nguyen, U of Washington, WA
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