Hello Di Nguyen,

The output of the "Feature coverage" tool is a tab-delimited file, so it will work with many of the tools in Statistics, Join, Subtract and Group, Filter and Sort, and Text Manipulation plus others.


"Subtract and Group -> Group" may be a good place to start. Please see the screencast "Tool tutorials -> Grouping" for an example about how to use the tool:
http://galaxyproject.org/wiki/Learn/Screencasts

Best,

Jen
Galaxy team

On 10/5/11 2:25 PM, Di Nguyen 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
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