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

[Jennifer Jackson]

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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-- 
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/Support