You need to examine the description page for the track in question to see what
they mean by 3000 and 0.5. You should find descriptions of what the data is
and how it was constructed, and references to papers written for the experiment.
The format of these files has nothing to do with what the numbers mean.
To get to the description page from the genome browser display, click on the
track button on the left margin of the genome browser graphic image. For
example:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeHistoneSuper
which leads to:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeBroadHistone
--Hiram
----- Original Message -----
From: "Radhouane Aniba" <[email protected]>
To: "Hiram Clawson" <[email protected]>
Cc: "Genome List" <[email protected]>
Sent: Saturday, January 14, 2012 11:11:14 PM
Subject: Re: [Genome] Wig, bigwig, bedgraph, in depth documentation
Thanks Hiram,
I went through your link, but it still doesn't answer my question, it is still
focused on the format. Let me ask the question again, in a wiggle file, in a
given position of the genome, what does it mean to have a value of 3000 and
what does it mean to have a value of 0.5 in another position of the genome for
a track let's say representing a histone modification mark.?
Rad
On Jan 14, 2012, at 11:52 PM, Hiram Clawson <[email protected]> wrote:
> These data file formats allow an experimenter to display data values at base
> positions.
> The data values an experiment generates are a decision made by the
> experiment. The files are merely
> the delivery mechanism to get the data values into the genome browser. The
> data values have
> no meaning without reference to the experiment that produced them. When you
> are viewing
> one of these data tracks the data values are graphed along the genome at
> their respective
> positions. To discover the meaning behind the graph, examine the description
> page
> for the track to see what the experiment is graphing. See also:
>
> http://genomewiki.ucsc.edu/index.php/Selecting_a_graphing_track_data_format
>
> --Hiram
>
> ----- Original Message -----
> From: "Radhouane Aniba" <[email protected]>
> To: "Genome List" <[email protected]>
> Sent: Saturday, January 14, 2012 8:25:37 PM
> Subject: [Genome] Wig, bigwig, bedgraph, in depth documentation
>
> Hello everyone,
>
> All of us, at least people working on NGS data analysis, are familiar with
> these three data types, and we are refering to UCSC documentation to
> understand their content and meaning. That's nice, but still there is some
> black boxes not necessary clear especially these questions :
>
> how comes that these files generated for the same experiment by different
> programs, create different values and different distribution
> a question that is more related to these programs now, how are these files
> created from reads alignments ? What algorithm is behind these files ?
> documentation on the format are clear enough, but significance and meaning of
> the scores inside each file are not explained, what are these values
> referring to ?
> look at this sentence from UCSC " The BedGraph format allows display of
> continuous-valued data in track format. This display type is useful for
> probability scores and transcriptome data" : probability score ? Of what ?
> How ?
> I hope i am not merging a lot of questions in a single post, they are all
> related and i think it is worth mentionning them in block so that we can
> discuss them in the same time.
>
> Thanks for all.
>
> Rad
>
>
>
>
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