Re: Fwd: JBrowse: Strange peaks appear in WIG tracks

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Re: Fwd: JBrowse: Strange peaks appear in WIG tracks

Ian Holmes
Thanks David. I just committed a fix and closed the ticket. Best wishes, Ian

David Breimann wrote:

>
> The files are attached again. I hope you'd be able to recreate and solve
> the issue.
>
> Thanks,
> Dave
>
>
> ---------- Forwarded message ----------
> From: *David Breimann* <[hidden email]
> <mailto:[hidden email]>>
> Date: Wed, Oct 6, 2010 at 10:59 PM
> Subject: JBrowse: Strange peaks appear in WIG tracks
> To: Mitch Skinner <[hidden email]
> <mailto:[hidden email]>>
> Cc: Ian Holmes <[hidden email] <mailto:[hidden email]>>
>
>
> Hi Mitch,
>
> I didn't send this to the mailing list to avoid sharing the large files
> with everyone, but feel free to cc your reply to the list.
>
> I've encountered a strange phenomena: some peaks appear in tracks
> created from WIG files with no apparent reason. The WIG doesn't have any
> value that supports a "peak" in those positions.
>
> Recreate the situation:
> * start with a clean JBrowse clone.
> * prepare-refseq with the attached fasta file (in the archive).
> * wig-to-json with the attached WIG file (in the archive).
> * Now zoom in to position 68000. Attached is a print-screen of what I
> see. Inspect the WIG and see all the values at this area are 2-3 and
> there's no peak.
>
> Keep up the good work!
> Dave
>
>
>
> ------------------------------------------------------------------------
>

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Re: Fwd: JBrowse: Strange peaks appear in WIG tracks

David Breimann
Thank you very much Ian.

On Tue, Oct 12, 2010 at 1:38 AM, Ian Holmes <[hidden email]> wrote:
Thanks David. I just committed a fix and closed the ticket. Best wishes, Ian

David Breimann wrote:

The files are attached again. I hope you'd be able to recreate and solve the issue.

Thanks,
Dave


---------- Forwarded message ----------
From: *David Breimann* <[hidden email] <mailto:[hidden email]>>
Date: Wed, Oct 6, 2010 at 10:59 PM
Subject: JBrowse: Strange peaks appear in WIG tracks
To: Mitch Skinner <[hidden email] <mailto:[hidden email]>>
Cc: Ian Holmes <[hidden email] <mailto:[hidden email]>>


Hi Mitch,

I didn't send this to the mailing list to avoid sharing the large files with everyone, but feel free to cc your reply to the list.

I've encountered a strange phenomena: some peaks appear in tracks created from WIG files with no apparent reason. The WIG doesn't have any value that supports a "peak" in those positions.

Recreate the situation:
* start with a clean JBrowse clone.
* prepare-refseq with the attached fasta file (in the archive).
* wig-to-json with the attached WIG file (in the archive).
* Now zoom in to position 68000. Attached is a print-screen of what I see. Inspect the WIG and see all the values at this area are 2-3 and there's no peak.

Keep up the good work!
Dave



------------------------------------------------------------------------



------------------------------------------------------------------------------
Beautiful is writing same markup. Internet Explorer 9 supports
standards for HTML5, CSS3, SVG 1.1,  ECMAScript5, and DOM L2 & L3.
Spend less time writing and  rewriting code and more time creating great
experiences on the web. Be a part of the beta today.
http://p.sf.net/sfu/beautyoftheweb
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Gmod-ajax mailing list
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