Hello Di,

Yes, the 200 bp windows should be for the reference genome, apologies if that was not clear.


The idea is to create a simple text file of the chrom-start-stop (one line per chromosome), upload, convert to BED, then create windows. Or better and less manually, you can extract the "chromInfo" table from the UCSC Table Browser (since you are using mm9, sourced from UCSC), do a few text edits to format, and use that as the BED file to create windows.

Once you have the 200 bp windows as the "target ranges" for the regional variation tool, compare your "query alignments" (BAM/SAM->Interval dataset) to get coverage. Group per window, per chrom, or however you wish with the tools I mentioned. If using "Group", the other data points are the numbers that can be graphed or manipulated. But that is just one suggestions, once you have the data in the right format (tabular), trying out different tools should be quick to do and tune/evaluate.

Good luck with the project,

Jen
Galaxy team

On 10/5/11 3:19 PM, Di Nguyen wrote:
Hi Jen,

Why is that when I made 200bp windows using "gro-seq.bed" file (my data
file), it came up empty? Did I think about this the wrong way, my 200bp
window supposes to be my reference genome, in this case mm9?

Secondly, when using regional variation, can I use a reference genome
such as mouse, and how do I created interval file for mm9, for example?

Thank you,

Di

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