Download bigwig file using TrackDumper plugin?

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Download bigwig file using TrackDumper plugin?

Haiming Wang
Hi,

Can anyone point me out if it's possible to download RNASeq data (bigwig files) in GBrowse? I tried TrackDumper plugin and it generated a conf without coverage data.

Thanks,
-Haiming

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Re: Download bigwig file using TrackDumper plugin?

Timothy Parnell
Hi Haiming,

It is supposed to. Take a closer look at the file TrackDumper generated and downloaded. There will be configuration stanzas at the top, but near the bottom there should be GFF3 annotation lines. One of those lines will represent the bigWig data and have a coverage attribute with the scores across the requested interval. Depending upon how the track was set up, it may or may not have an informative source, type, or name attribute; you will have to look carefully. Note that the coverage attribute will have the number of data points equal to the width in pixels GBrowse is displaying, irrespective of the original source file.

You can also try using the little download (floppy) icon in the track title. This will download the bigWig data in bedGraph format, and will be a straight dump from the bigWig file.

Hope that helps.

Tim

On Jan 16, 2014, at 7:57 AM, Haiming Wang <[hidden email]> wrote:

> Hi,
>
> Can anyone point me out if it's possible to download RNASeq data (bigwig files) in GBrowse? I tried TrackDumper plugin and it generated a conf without coverage data.
>
> Thanks,
> -Haiming
> ------------------------------------------------------------------------------
> CenturyLink Cloud: The Leader in Enterprise Cloud Services.
> Learn Why More Businesses Are Choosing CenturyLink Cloud For
> Critical Workloads, Development Environments & Everything In Between.
> Get a Quote or Start a Free Trial Today.
> http://pubads.g.doubleclick.net/gampad/clk?id=119420431&iu=/4140/ostg.clktrk_______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse


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Re: Download bigwig file using TrackDumper plugin?

Haiming Wang
Thanks a lot Tim! I updated the TrackDumper and it's working fine now.

-Haiming


On Thu, Jan 16, 2014 at 11:24 AM, Timothy Parnell <[hidden email]> wrote:
Hi Haiming,

It is supposed to. Take a closer look at the file TrackDumper generated and downloaded. There will be configuration stanzas at the top, but near the bottom there should be GFF3 annotation lines. One of those lines will represent the bigWig data and have a coverage attribute with the scores across the requested interval. Depending upon how the track was set up, it may or may not have an informative source, type, or name attribute; you will have to look carefully. Note that the coverage attribute will have the number of data points equal to the width in pixels GBrowse is displaying, irrespective of the original source file.

You can also try using the little download (floppy) icon in the track title. This will download the bigWig data in bedGraph format, and will be a straight dump from the bigWig file.

Hope that helps.

Tim

On Jan 16, 2014, at 7:57 AM, Haiming Wang <[hidden email]> wrote:

> Hi,
>
> Can anyone point me out if it's possible to download RNASeq data (bigwig files) in GBrowse? I tried TrackDumper plugin and it generated a conf without coverage data.
>
> Thanks,
> -Haiming
> ------------------------------------------------------------------------------
> CenturyLink Cloud: The Leader in Enterprise Cloud Services.
> Learn Why More Businesses Are Choosing CenturyLink Cloud For
> Critical Workloads, Development Environments & Everything In Between.
> Get a Quote or Start a Free Trial Today.
> http://pubads.g.doubleclick.net/gampad/clk?id=119420431&iu=/4140/ostg.clktrk_______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse



------------------------------------------------------------------------------
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Learn Why More Businesses Are Choosing CenturyLink Cloud For
Critical Workloads, Development Environments & Everything In Between.
Get a Quote or Start a Free Trial Today.
http://pubads.g.doubleclick.net/gampad/clk?id=119420431&iu=/4140/ostg.clktrk
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