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 ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:

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