Qs regarding the Broad Histone (wgEncodeBroadHistone) Track Description

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Yafit Steinberg

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May 27, 2013, 4:08:21 PM5/27/13

to gen...@soe.ucsc.edu

Hello,

I downloaded data from the Broad Histone (wgEncodeBroadHistone) Track Description.

I'd like to kindly ask the following:

1) I understand that the score associated with each enriched interval is the mean signal value across the interval. Yet, as to the actual values – what are exactly the units? Is it the ratio between signals? Is it the ratio between actual numbers of reads? Is it in linear scale?

2) Similarly – what is 'wiggle', and how do you calculate 'read density'? What is the nature of the 'Signal' values?

Thanks, Y. Steinberg

Steve Heitner

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May 31, 2013, 5:22:13 PM5/31/13

to Yafit Steinberg, gen...@soe.ucsc.edu

Hello, Yafit.

Wiggle refers to a specific data file format. For more information about the wiggle file type, please see http://genome.ucsc.edu/goldenPath/help/wiggle.html.

For specific questions regarding the Broad Histone data, I recommend directly contacting the lab that produced the data. Each ENCODE track description page has a Credits section that contains the appropriate contact information. In this case, the description page is located at http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeBroadHistone.

Please contact us again at gen...@soe.ucsc.edu if you have any further questions.

---
Steve Heitner
UCSC Genome Bioinformatics Group

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