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