[Useq-users] Making Random Regions for the IntersectRegions application

[David N. <dav...@gm...>]

------ Forwarded Message
From: David Nix <dav...@hc...>
Date: Tue, 25 May 2010 07:43:57 -0600
To: Ravi Alla <Rav...@hc...>
Conversation: random chromosomes
Subject: Re: random chromosomes

You need a folder containing chromosome split files (chr1, chr2, chr3, ...).
These represent regions that were possibly interrogated (sequenced) in your
dataset where each file contains three tab delimited columns (chr start
stop).    The easiest way to make these is to pool all of your PointData
into a hypothetical ³treatment² sample, run ScanSeqs on this sample using
the peak shift and window size you used in your analysis, then run the
EnrichedRegionMaker selecting enriched regions with 1 or more reads.  You¹ll
then need to parse the gff or egr file from the EnrichedRegionMaker using
the PrintSelectColumns app to extract just the chr, start, and stop columns.
Then split the parsed file by chromosome using a shell script.  For example:

³for x in 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19  X Y M; do echo
chr$x; cat myParsedFile.txt | grep ­w chr$x  > chr$x; done²

-cheers, D



On 5/24/10 4:46 PM, "Ravi Alla" <Rav...@hc...> wrote:

> Hi David,
> I was wondering how one would go about making a random chromosomes folder, to
> use in IntersectRegions. I want to make one for mouse.
> Thanks
> Ravi 
> 

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