[Genome] What is the difference between the wiggle format and bedGraph format?

[Peng Yu]

I see the following description.

http://genome.ucsc.edu/goldenPath/help/bedgraph.html

"This track type is similar to the wiggle (WIG) format, but unlike the
wiggle format, data exported in the bedGraph format are preserved in
their original state."

But it is not making sense to me what the difference between wiggle
and bedGraph is. What does 'original state' mean? Could the
description on the webpage be revised to make it clearer?

[Hiram Clawson]

Good Morning:

Wiggle tracks compress the data for storage and reduce
the precision of the input data values. The exact
data values can not be recovered from the compression
format. The bedGraph type of tracks store and use the
actual original data. Thus, the bedGraph tracks can
return the original data in the table browser.

See also:
http://genome.ucsc.edu/goldenPath/help/wiggle.html
http://genomewiki.ucsc.edu/index.php/Selecting_a_graphing_track_data_format
http://genomewiki.ucsc.edu/index.php/Wiggle

--Hiram

[Jennifer Jackson]

Hello Peng,
The formats are related, but not identical.

Wiggle data come in several times, many times compressed to format to view in the browser. The original state of the data is still wiggle, just an uncompressed version. This is in the documentation. Also note that the uncompressed version on many wiggle tracks is available on Downloads.

If you want to visualize this, pick a range from the mySQL database of a wiggle track and compare to the same range of the uncompressed version from downloads.

Here is a good pair to compare with the actual command used: gc5Base.txt.gz

Original state:
http://hgdownload.cse.ucsc.edu/goldenPath/hg18/gc5Base/ (file in here w/ README)

Wiggle:
http://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/ file in here w/ schema and README)

bedGraphs is another format, designed for data that is not appropriate to view in a compressed state and is better for large datasets (as stated in the FAQ - an example is when there is one value for every base).

Another compression format is bigWig.

Each of these formats has a description for the actual columns and format and some discussion is provided on tool pages (such as custom tracks) about when to use which. This descriptions here are good: http://genome.ucsc.edu/FAQ/FAQformat#format6

Hope this helps,
Jennifer

------------------------------------------------
Jennifer Jackson
UCSC Genome Bioinformatics Group

----- "Peng Yu" <peng...@gmail.com> wrote:

> From: "Peng Yu" <peng...@gmail.com>
> To: gen...@soe.ucsc.edu
> Sent: Friday, December 18, 2009 8:26:22 AM GMT -08:00 US/Canada Pacific
> Subject: [Genome] What is the difference between the wiggle format and bedGraph format?
>
> I see the following description.
>
> http://genome.ucsc.edu/goldenPath/help/bedgraph.html
>
> "This track type is similar to the wiggle (WIG) format, but unlike
> the
> wiggle format, data exported in the bedGraph format are preserved in
> their original state."
>
> But it is not making sense to me what the difference between wiggle
> and bedGraph is. What does 'original state' mean? Could the
> description on the webpage be revised to make it clearer?

> _______________________________________________
> Genome maillist - Gen...@lists.soe.ucsc.edu
> https://lists.soe.ucsc.edu/mailman/listinfo/genome