[Gmod-help] Many Features

[Lincoln Stein]

Hi Todd,

The bumping algorithm will definitely die if you try to put too many
features into a single track. The algorithm could be made much more
efficient if we guarantee that names and descriptions won't be printed on
the features.

What I'm doing in my own lab is not trying to show the overlapping features
directly, but instead to show a density plot of the number of times a base
pair was touched. I have plans to work on a glyph to highlight SNPs and
other variations, but I haven't started on it.

Lincoln

On Jan 21, 2008 1:59 PM, <todd.moughamer at syngenta.com> wrote:

>  Hi,
>
> I am attempting test Gbrowse's ability to render next gen sequencing
> data...particularly short reads. I simulated thousands of short overlapping
> 35 bp features over a 135 bp sequence. If I try to render them on one track
> the best I can do is to set the number of features cut off to 25…with the
> remaining features being condensed on to one line. Increasing the cut off
> results in a timeout. Rendering data on separate tracks would seem
> impractical since you would have to add a line in the conf file for each.
> Any suggestions?
>
> Todd
>
> *Todd Moughamer*
>
> Bioinformatics Consultancy & Training Group
>
> Syngenta Biotechnology, Inc.
>
> 3054 Cornwallis Road, 1243.E
>
> Research Triangle Park, NC 27709-2257
>
> Tel: 919-597-3078
>
> Email: todd.moughamer at syngenta.com
> ***www.syngenta.com*****
>
>


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Lincoln D. Stein
Cold Spring Harbor Laboratory
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