gbrowse wiggle_xyplot.
|
View:
New views
4 Messages
—
Rating Filter:
Alert me
|
 |
gbrowse wiggle_xyplot.
by vipin.ts
::
Rate this Message:
Hi all,
I would like to represent short read coverage through gbrowse. Here I used the sample input file descried below. track type=wiggle_0 name=sample variableStep chrom=I span=10 557 1 variableStep chrom=I span=10 622 1000 variableStep chrom=I span=10 653 2000 variableStep chrom=I span=10 658 3000 variableStep chrom=I span=10 757 4000 Then I made edit in the config file and when I browse through the region of the specified chromosome, the wiggle_xyplot appears. But the problem is in the representation of 'y axis' unit in the graph. From the example file I can see that y value is varying from 1 to 4000. but in display I can see only one unit in xy plot. I gave min_score and max_score 0 and 10 respectively in the config file. It will be great if anyone can help me in the same. Thanks in advance, Vipin T S ------------------------------------------------------------------------------ Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
|
|
Re: gbrowse wiggle_xyplot.
by Scott Cain-4
::
Rate this Message:
Hello Vipin,
Did you sort this out? I don't know exactly what the problem is, but I can tell you that your wiggle file doesn't look like the examples on the gmod.org wiki: http://gmod.org/wiki/GBrowse/Uploading_Wiggle_Tracks and that may cause problems. Scott On Mon, Sep 7, 2009 at 4:27 AM, Vipin TS <vipin.ts@...> wrote: > Hi all, > > I would like to represent short read coverage through gbrowse. Here I used > the sample input file descried below. > > track type=wiggle_0 name=sample > variableStep chrom=I span=10 > 557 1 > variableStep chrom=I span=10 > 622 1000 > variableStep chrom=I span=10 > 653 2000 > variableStep chrom=I span=10 > 658 3000 > variableStep chrom=I span=10 > 757 4000 > > Then I made edit in the config file and when I browse through the region of > the specified chromosome, the wiggle_xyplot appears. > > But the problem is in the representation of 'y axis' unit in the graph. > From the example file I can see that y value is varying from 1 to 4000. but > in display I can see only one unit in xy plot. I gave min_score and > max_score 0 and 10 respectively in the config file. > > It will be great if anyone can help me in the same. > > Thanks in advance, > Vipin T S > > > ------------------------------------------------------------------------------ > Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day > trial. Simplify your report design, integration and deployment - and focus > on > what you do best, core application coding. Discover what's new with > Crystal Reports now. http://p.sf.net/sfu/bobj-july > _______________________________________________ > Gmod-gbrowse mailing list > Gmod-gbrowse@... > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research ------------------------------------------------------------------------------ Come build with us! The BlackBerry® Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9-12, 2009. Register now! http://p.sf.net/sfu/devconf _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
|
|
Re: gbrowse wiggle_xyplot.
by vipin.ts
::
Rate this Message:
Hi Scott,
It was problem with my input file. In my file variableStep chrom=I span=10 stanza was repeating. I found that variableStep support only a fixed span length. Thanks for your help. Regards, Vipin T S 2009/9/16 Scott Cain <scott@...> Hello Vipin, -- Vipin T S Friedrich Miescher Laboratory of the Max Planck Society Spemannstrasse 39, 72076 Tuebingen, Germany Tel:+49 7071 601 824 ------------------------------------------------------------------------------ Come build with us! The BlackBerry® Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9-12, 2009. Register now! http://p.sf.net/sfu/devconf _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
|
|
Re: gbrowse wiggle_xyplot.
by Lincoln Stein-3
::
Rate this Message:
Hi,
If you can get your data into BAM format, then there is an adaptor in GBrowse that will read the BAM files and directly render coverage tracks on the fly. Lincoln On Mon, Sep 7, 2009 at 4:27 AM, Vipin TS <vipin.ts@...> wrote: Hi all, -- Lincoln D. Stein Director, Informatics and Biocomputing Platform Ontario Institute for Cancer Research 101 College St., Suite 800 Toronto, ON, Canada M5G0A3 416 673-8514 Assistant: Renata Musa <Renata.Musa@...> ------------------------------------------------------------------------------ Come build with us! The BlackBerry® Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9-12, 2009. Register now! http://p.sf.net/sfu/devconf _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
| Free embeddable forum powered by Nabble | Forum Help |
