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@manipal.edu


      
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