[Genome] About Affy all Exon (11 tissue)

[Andy Pohl]

Yes thickStart = chromStart and thickEnd = chromEnd for all exons.
thickStart/End are mainly to distinguish between the promoter/UTR and
the CDS portion of a gene.  The thicker display is the CDS.  This
comes up in other tracks... mostly the gene tracks.  In this case, the
exons are all supposed to be coding, so the thickStart/End fields are
useless, but that's just been a data format we've been using for a
long time.

You've come across a known problem I'm supposed to fix and I'm sorry
for the confusion.  Take a look at this page:

http://genomewiki.cse.ucsc.edu/index.php/Microarray_track

It describes the microarray track and the example used for the
microarrayGroups.ra is actually the Affy All Exon track.  Sorry about
that.  This should really be a part of the table download.

Andy Pohl
UCSC CBSE

On 10/19/07, Li, Dong <dli at msm.edu> wrote:
> To the UCSC genome browser team,
>
> First of all thanks for your very nice interface to the genome, I love it!
>
> I have a question on the Affymetrix Human Extron data that can be downloaded
> via the table browser. The table I get out have the following fields :
>
> bin     chrom   chromStart      chromEnd        name    score   strand  thickStart thickEnd reserved    blockCount      blockSizes      chromStarts     expCount  expIds expScores
>
> For the expIds field I get numbers corresponding to the different
> tissues(11 tissues, 3 replicate experiments were done for a total of 33 arrays), but I don't known which numbers correspond to which tissue.
>
> Where do I get this Information?
>
> In adddition, I noted that thickStart always have the same number as chromStart and thickEnd always have the same number as chromEnd, it always like that. or thickStart and thickEnd have specific meaning.
>
> Thanks in advance,
>
> I would like to hearing from you as soon as poosible.
>
> Dong Li Ph.D.
>
>
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