Question: How To Count Reads In 200Bp Windows And Save The Output Per Chromosome?
7.2 years ago by
Di Nguyen • 50
Di Nguyen • 50 wrote:
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
ADD COMMENT • link •modified 7.2 years ago by Jennifer Hillman Jackson ♦ 25k • written 7.2 years ago by Di Nguyen • 50