[GET-dev] GFF3 to Wig ?

Madeleine Ball mpball at gmail.com
Tue May 24 11:03:16 EDT 2011

> Does CGI only provide evidence for called alleles, or is this merely done to
> make the example data smaller?

The best people to ask would be CGI themselves, of course; I recommend
their training / user meetings, super informative.

It does look like the online examples are only the "ASM" directory --
what you want is data from the LIB and MAP directories -- these do end
up being huge so I think you're right that they didn't put them up
because it's too large. In the past (at their training sessions) CGI
has provided an example of full data (LIB and MAP as well as ASM) for
chr21 of NA19240. I'm not finding any copies of this on either ftp or
ftp2 sites ... if you want to read about it, you can click the
"documentation" tab on the downloads page to get some description of
the LIB & MAP data.

You should ask CGI to add a full data chr21 sample to their ftp site.
I could try to dig up one of ours for you, but I'd rather we all push
the sequencing companies to make public examples of their data sets.
(Last I checked Illumina's service fails to do this.) CGI has
generally been very good about this, so hopefully they'll be
responsive. If they aren't, report back, and the rest of us can chime
in. :-)

  -- Madeleine

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