[BioC] Help on ChIPpeakAnno

[Zhu, Lihua (Julie)]

Prashantha,

Could you please send us the session information and the code snippet with
the example coordinates? Thanks!

Best regards,

Julie


On 3/9/11 3:33 AM, "Prashantha Hebbar" <prashantha.hebbar at yahoo.com> wrote:

> Dear all,
> 
> I have few issues with TSS information obtained through ChIPpeakAnno. To
> catalog 
> TSS information pertaining to my probe sets I have used TSS.human.GRCh37
> (ensemble) build. After obtaining information, data in the columns
> distanceToFeature and shorstestDistance do not exactly match with either
> SwitchGear TSS prediction available through UCSC or Eponine tss prediction
> available through Ensemble.
> 
> 
> Here is one such example I have encountered.
> To coordinate chr11:128391471-128391952, ChIPpeakAnno gave distanceToFeature
> as 
> 65982 and shorstestDistance as 62815. The given coordinate is from
> chr11:128328656-128457453 (ETS1). if we search with same coordinate in either
> UCSChg19(SwitchGear) or Ensemble (Eponine), for TSS, tss situates at 128392173
> position. if we subtract 128392173-128328656=63517. This in contradiction not
> matching to the ChIPpeakAnno (65982).
> 
> Can anybody please clarify this issue? How come with same build this
> difference? 
> 
> 
> Thanking you in anticipation.
> 
> Regards,
> Prashantha
> 
> Manipal Life Sciences Center,
> Manipal University,
> Manipal, India
> PIN: 576104
> Email:prashantha.hebbar at manipal.edu
> 
> 
>       
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> 
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