Hi Jason,
I'll do a fresh install and try it. There has been a lot of flux in the
wiggle code base in the last week as we load and debug the modENCODE data.
Lincoln
On Thu, Feb 21, 2008 at 8:41 PM, Jason Stajich <[EMAIL PROTECTED]> wrote:
>
> If I generate a binary .wig file from the microarray.wig file with
> wiggle2gff3, the binary is larger on my machine than the one that comes in
> CVS.
>
> However neither seem to really work for me, here is the volvox tutorial:
> http://tinyurl.com/2skylj
> http://tinyurl.com/2qke
> If you zoom out to 2KB there is no image at all.
>
> When I do the same thing with my phastcons data I see nothing at any zoom.
> Is there an easy way to debug the feature through a callback to see
> whether or not there are any features being retrieved through the wiggle
> interface?
>
> Can anyone else confirm a fresh-install + the wiggle in volvox tutorial
> working for them?
>
> Thanks,
> -jason
>
> On Feb 20, 2008, at 12:50 PM, Lincoln Stein wrote:
>
> Hi Jason,
>
> If you do a CVS update you'll find sample files and a walkthrough in the
> tutorial. If you tried this today after I worked on Sean's slow-loading
> issue, there is a finite chance that I inadvertently broke something.
>
> Lincoln
>
> On Feb 20, 2008 3:40 PM, Jason Stajich <[EMAIL PROTECTED]> wrote:
>
> I've loaded a small file of phastcons results that I generated and I
> don't see any values in with the wiggle_xyplot and when I use the
> wiggle_density it is empty.
> Is there any way to debug that features that are loaded and available
> to the glyph?
>
> Are there example conf files stanzas for different wiggl data that
> can be put on the wiki?
>
> thanks,
> -jason
>
>
> On Feb 19, 2008, at 4:33 AM, Sean O'Keeffe wrote:
>
> Hi all,
> I'm currently tasked with displaying phastCons data in Gbrowse. I'm
> using Bio::Graphics::Wiggle::Loader to load each data set
> (chromosome.pp
> file). Has anyone done this before or give me an estimate on the time
> needed? I started on Friday evening with chr1.pp and it's still
> loading
> the *.wig file.
> chr1.pp is ~1.4GB in size as is chr2.pp but the chromosome size gets
> progessively smaller. I've got this this job running on a 6ghz dual
> core
> linux with 4gb of memory.
>
> Thanks,
> Sean.
>
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>
>
>
> --
> Lincoln D. Stein
> Cold Spring Harbor Laboratory
> 1 Bungtown Road
> Cold Spring Harbor, NY 11724
> (516) 367-8380 (voice)
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> FOR URGENT MESSAGES & SCHEDULING,
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>
>
>
--
Lincoln D. Stein
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724
(516) 367-8380 (voice)
(516) 367-8389 (fax)
FOR URGENT MESSAGES & SCHEDULING,
PLEASE CONTACT MY ASSISTANT,
SANDRA MICHELSEN, AT [EMAIL PROTECTED]
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