Need some help - submitting TopoView RNA-seq stuff to GMOD

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Need some help - submitting TopoView RNA-seq stuff to GMOD

vstrelet

Hi guys,

Talking to Josh Goodman after his visit to ISMB we realized
that it might be the right time to submit to GMOD our
TopoView thing which FlyBase uses to display RNA-seq
data in GBrowse.

Thingie is not fully ready for any kind of responsible submission
as processing of every new wig resource turns to be a real pain
(looks like every wig submission in fact uses different file
format) therefore requiring developer assistance (writing separate
block of code handling data of that particular submission).

But the reason to start this submission is that Josh assured me
that several (?) people expressed readiness to take proper care of
such additional development until thing becomes a package
capable of handling all formats without need of detailed
developer support.

So this is a request for interested people to reply and to start
exchange to determine what exactly should be done - it turned
out that there is no instruction on glyph (or even adaptor)
submission and requirements anywhere on the GMOD-GBrowse
page..

I'm ready to write detailed explanations of how it works, what
the final data format is (and why) and to submit
  - example wig file (or several different)
  - resulting data file (for fast retrievals)
  - indexing script which converts wig into required data file
  - glyph which is doing all the painting
  - config showing how all that is activated
Then I'm thinking about assisting interested people in debugging,
to get their GBrowse to the condition when test data shows up fine
as a TopoView track in display, and then hopefully to bail out of
any intense development/debugging activity.
If this is not how it will happen - just correct me guys, I'll
cooperate..:))

Help to hear from somebody soon,

Regards,

Victor Strelets
FlyBase Consortium

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Re: Need some help - submitting TopoView RNA-seq stuff to GMOD

Dave Clements, GMOD Help Desk-3
Hi Victor,

Have you got any response to this question?  If not, I can feature it on the GMOD website to draw more attention to it.  There are indeed a lot of users out there who could use this.

Thanks,

Dave C

On Fri, Jul 23, 2010 at 1:52 PM, vstrelet <[hidden email]> wrote:

Hi guys,

Talking to Josh Goodman after his visit to ISMB we realized
that it might be the right time to submit to GMOD our
TopoView thing which FlyBase uses to display RNA-seq
data in GBrowse.

Thingie is not fully ready for any kind of responsible submission
as processing of every new wig resource turns to be a real pain
(looks like every wig submission in fact uses different file
format) therefore requiring developer assistance (writing separate
block of code handling data of that particular submission).

But the reason to start this submission is that Josh assured me
that several (?) people expressed readiness to take proper care of
such additional development until thing becomes a package
capable of handling all formats without need of detailed
developer support.

So this is a request for interested people to reply and to start
exchange to determine what exactly should be done - it turned
out that there is no instruction on glyph (or even adaptor)
submission and requirements anywhere on the GMOD-GBrowse
page..

I'm ready to write detailed explanations of how it works, what
the final data format is (and why) and to submit
 - example wig file (or several different)
 - resulting data file (for fast retrievals)
 - indexing script which converts wig into required data file
 - glyph which is doing all the painting
 - config showing how all that is activated
Then I'm thinking about assisting interested people in debugging,
to get their GBrowse to the condition when test data shows up fine
as a TopoView track in display, and then hopefully to bail out of
any intense development/debugging activity.
If this is not how it will happen - just correct me guys, I'll
cooperate..:))

Help to hear from somebody soon,

Regards,

Victor Strelets
FlyBase Consortium

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View this message in context: http://generic-model-organism-system-database.450254.n5.nabble.com/Need-some-help-submitting-TopoView-RNA-seq-stuff-to-GMOD-tp1869209p1869209.html
Sent from the gmod-gbrowse mailing list archive at Nabble.com.

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Re: Need some help - submitting TopoView RNA-seq stuff to GMOD

vstrelet
On Wednesday July 28 2010 12:48 pm, Dave Clements, GMOD Help Desk wrote:
> Have you got any response to this question?  If not, I can feature it on
> the GMOD website to draw more attention to it.  There are indeed a lot of
> users out there who could use this.

No Dave, not a single one..

Go ahead with your idea about GMOD site.

Alternative will be me re-writing data conversion
script into something simpler, to handle just one (!)
flavor of cov/wig file and supplying detailed description
(and sample) of the resulting file format and then submitting
that + glyph to guys you for distribution. With a warning that
users apply that conversion script at their own risk and should
be ready to adjust its code to handle format variations, if necessary.
This is because glyph itself and its config  control  both work
just fine already, and the only problem is in data conversion
script handling multiple flavors of cov/wig format.

Victor

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