[Catch-users] How to convert TXT or BAR files to WGI files?

[Fiona Nielsen]

In reply to Marco-Antonio,

Thanks for posting your question to the CATCH-users mailing list!

I do not know the format that Affymetrix uses for their data, but the
format you need (the wiggle format) is described here:

http://genome.ucsc.edu/goldenPath/help/wiggle.html

It is actually BED format, with one signal value for each chromosome
position. If this is not the format that you already have in one of
the files you mention, you will need to reformat your data using e.g.
a perl or commandline script before you load it into CATCH.

Best,

-Fiona-


On Sun, Nov 23, 2008 at 4:24 PM, Marco-Antonio wrote:
> Dear CATCH members,
>
> I found this tool quite interesting and promising for the analysis of our
> ChIP-seq /ChIP-chip data. Nevertheless for the moment I have a big problem,
> which is how to convert the output data from our current working plattform,
> namely Affymetrix or SOLEXA, to WIG files that could then load them into
> CATCH. From affymetrix I can get either TXT or Bar files...of course I have
> also the intitial CEL files but I think CATCH requires pre-normalized data
> or?. Then could some one give me a hit about converting either TXT or BAR
> files to WIG files...I can generate BED files with the IGB software then, Im
> only missing the WGI files to star to play with CATCH.
> Thanks for your help guys.
>