Re: wiggle_xyplot suggestions for ChIP-seq data

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Re: wiggle_xyplot suggestions for ChIP-seq data

Stephen Taylor
Hi Lincoln,

> Very good suggestions. I'm playing around with chip-seq visualization
> now, so this is timely.

Has this been written

>         * Allow the reads to be artificially extended past their 3' end by X
>           bp before plotting the overlap density. This is a trick used to
>           make ChIP-seq peaks stand out more. The underlying rational is
>           that you are plotting the ChIP-enriched DNA fragments (where X bp
>           is an approximation of the average fragment length) as opposed to
>           just the short end of the fragment that you sequenced.

?  This would be extremely useful.

Thanks,

Steve


>
> Lincoln
>
> On Fri, Jan 29, 2010 at 4:37 PM, Shaun Mahony <[hidden email]
> <mailto:[hidden email]>> wrote:
>
>     Here are a couple of suggestions for wiggle_xyplot options that would be
>     particularly useful in the context of ChIP-seq data. You'll often seen
>     publication figures that make use of these ideas:
>
>         * Separate read density according to strandedness; plot forward
>           strand reads above the line in one color and reverse strand reads
>           below the line in another. This is similar to what Yufeng
>           suggested yesterday. It would be useful for visualizing TF binding
>           events where the actual bound bases should be between a stack of
>           forward reads and a stack of reverse reads (see Fig 1 in this
>           paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2532738/)
>         * Allow the reads to be artificially extended past their 3' end by X
>           bp before plotting the overlap density. This is a trick used to
>           make ChIP-seq peaks stand out more. The underlying rational is
>           that you are plotting the ChIP-enriched DNA fragments (where X bp
>           is an approximation of the average fragment length) as opposed to
>           just the short end of the fragment that you sequenced.
>
>
>     Shaun Mahony
>
>
>     ------------------------------------------------------------------------------
>     The Planet: dedicated and managed hosting, cloud storage, colocation
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>     Choose flexible plans and management services without long-term
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>     away.
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>     [hidden email]
>     <mailto:[hidden email]>
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>
>
>
>
> --
> 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 <[hidden email]
> <mailto:[hidden email]>>


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Re: wiggle_xyplot suggestions for ChIP-seq data

Lincoln Stein
No, it isn't written yet. This code actually needs to be incorporated into the tools that calculate coverage from nextgen read data. Straightforward, but I've got a few bugs to fix first.

Lincoln

On Thu, May 20, 2010 at 9:49 AM, Steve Taylor <[hidden email]> wrote:
Hi Lincoln,

> Very good suggestions. I'm playing around with chip-seq visualization
> now, so this is timely.

Has this been written

>         * Allow the reads to be artificially extended past their 3' end by X
>           bp before plotting the overlap density. This is a trick used to
>           make ChIP-seq peaks stand out more. The underlying rational is
>           that you are plotting the ChIP-enriched DNA fragments (where X bp
>           is an approximation of the average fragment length) as opposed to
>           just the short end of the fragment that you sequenced.

?  This would be extremely useful.

Thanks,

Steve


>
> Lincoln
>
> On Fri, Jan 29, 2010 at 4:37 PM, Shaun Mahony <[hidden email]
> <mailto:[hidden email]>> wrote:
>
>     Here are a couple of suggestions for wiggle_xyplot options that would be
>     particularly useful in the context of ChIP-seq data. You'll often seen
>     publication figures that make use of these ideas:
>
>         * Separate read density according to strandedness; plot forward
>           strand reads above the line in one color and reverse strand reads
>           below the line in another. This is similar to what Yufeng
>           suggested yesterday. It would be useful for visualizing TF binding
>           events where the actual bound bases should be between a stack of
>           forward reads and a stack of reverse reads (see Fig 1 in this
>           paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2532738/)
>         * Allow the reads to be artificially extended past their 3' end by X
>           bp before plotting the overlap density. This is a trick used to
>           make ChIP-seq peaks stand out more. The underlying rational is
>           that you are plotting the ChIP-enriched DNA fragments (where X bp
>           is an approximation of the average fragment length) as opposed to
>           just the short end of the fragment that you sequenced.
>
>
>     Shaun Mahony
>
>
>     ------------------------------------------------------------------------------
>     The Planet: dedicated and managed hosting, cloud storage, colocation
>     Stay online with enterprise data centers and the best network in the
>     business
>     Choose flexible plans and management services without long-term
>     contracts
>     Personal 24x7 support from experience hosting pros just a phone call
>     away.
>     http://p.sf.net/sfu/theplanet-com
>     _______________________________________________
>     Gmod-gbrowse mailing list
>     [hidden email]
>     <mailto:[hidden email]>
>     https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>
>
>
> --
> 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 <[hidden email]
> <mailto:[hidden email]>>


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--
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 <[hidden email]>

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