[Genome] What up with the #bin?

[Galt Barber]

A little note:

The paper calls the first bin 1,
but in our code the first bin is 0.

-Galt


On Wed, 14 May 2008, Hiram Clawson wrote:

> Good Morning Dr. Becker:
>
> This is a scheme to speed up MySQL queries.  Items are assigned
> to a bin based on their chromosome coordinate.
>
> As described in this paper:
> http://www.genome.org/cgi/content/abstract/12/6/996
> Genome Res. 2002 Jun;12(6):996-1006.
> The human genome browser at UCSC.
> Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D.
>
> Please note Figure 7 in that paper.  The scheme has been
> expanded since then to include one more top-level bin size of 4Gb.
> There is an exerciser and test program in the kent source
> tree src/hg/lib/tests/binTest.c
>
> --Hiram
>
> Becker, Kevin (NIH/NIA/IRP) [E] wrote:
>> Hello genome folks,
>>
>>
>>
>> In the UCSC table downloads, such as mgcGenes, the first column is #bin.
>>
>> What's that?
>>
>>
>>
>> Presumably genes are binned into groups, but how?
>>
>>
>>
>> Sincerely,
>>
>>
>>
>> KGB
>>
>>
>>
>> Kevin G. Becker Ph.D.
>> Head, Gene Expression and Genomics Unit
>> Deputy Chief, Research Resources Branch
>> NIH Biomedical Research Center
>>
>> 251 Bayview Boulevard, Room 4B211
>> National Institute on Aging
>> National Institutes of Health
>> Baltimore, MD 21224
>> TEL:   410-558-8360
>> FAX:  410-558-8236
>> beckerk at grc.nia.nih.gov <mailto:beckerk at grc.nia.nih.gov>
>> http://www.grc.nia.nih.gov/branches/rrb/dna/dna.htm
>> <http://www.grc.nia.nih.gov/branches/rrb/dna/dna.htm>
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>