[galaxy-user] How to count reads in 200bp windows and save the output per chromosome?

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