Hi, Nicolas.
1.) Structural variants apply to both strands, so there is no meaningful
strand for this data set. Unfortunately, in order to use itemRgb (BED
9), we need a placeholder value in the strand column, so it's always "+".
2.) Yes, there are 101605 rows in the table, each with the placeholder +.
3.) The stars are for a histogram -- but a histogram with one value
('+') isn't very interesting or useful. For a table with meaningful
strand, the relative proportion of '+' and '-' could be interesting. If
you click on the values link for the chrom field, you'll get a better
idea of what this feature is for.
If you have any additional questions, please reply to: [email protected]
-
Greg Roe
UCSC Genome Bioinformatics Group
On 7/16/12 8:40 AM, nicolas allias wrote:
> Hi all,
>
>
>
> First of all, I didn't found the information anywhere else, so please give
> me a link to the answer instead of yelling ;-)
>
>
>
> *Request* about tables descriptions documentation of DGV Struct Var (hg19).
>
> -> following the link 'info' about the strand line :
>
>
> <http://genome.ucsc.edu/cgi-bin/hgTables?hgta_database=hg19&hgta_histoTable=
> dgv&hgta_doValueHistogram=strand>
> http://genome.ucsc.edu/cgi-bin/hgTables?hgta_database=hg19&hgta_histoTable=d
> gv&hgta_doValueHistogram=strand
>
>
>
> I'd like some clarification :
>
> 1/ Why there is not '-' value in this info ? Truncated table ? It's my guess
> for the next.
>
>
>
> 2/ Count explanation.
>
> Count 101605
>
> This is the exact number of lines in the dgv table, right ? Does this means
> that there is exactly 101 605 '+' in the base, in this field ? (so all lines
> are supposed to be on the '+' strand).
>
>
>
> 3/ Starts everywhere !
>
> What is these 60 stars are supposed to mean ?
>
> graph
>
> ************************************************************
>
>
>
> Many thanks by advance for your time,
>
> Nicolas Allias
>
> _______________________________________________
> Genome maillist - [email protected]
> https://lists.soe.ucsc.edu/mailman/listinfo/genome
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