[Genome] Question regarding visualization of NimbleGen ChIP-chip data

[Hiram Clawson]

Good Afternoon Christoph:

Can you find some data on the DVD that has position and value ?
Something like a two column format.  Or perhaps something like
a four column format: chrom, start, end, value

If you can find the value data, that is most likely the wiggle
data you need to make a graph.  This is one of the standard
formats for custom tracks.

--Hiram

Christoph Bock wrote:
> Hello,
> 
> I was wondering how NimbleGen ChIP-chip data should best be imported into
> the UCSC Genome Browser, for visualization and analysis. The very simple
> approach - uploading the GFF files from the NimbleGen DVDs as custom tracks
> - doesn't really produce the desired result (it just displays the oligomer
> positions rather than their values).
> 
> I'm sure that you performed this task a hundred times during the ENCODE
> project, and I'd be grateful if you could give me a quick hint or even a set
> of scripts that help me prepare the standard NimbleGen DVD data (pair format
> or GFF format) for visualization in UCSC Genome Browser.
> 
> Thanks in advance!
>  Christoph
> 
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