[Bioperl-l] [Gmod-gbrowse] scores in Bio::DB::BigBed

[Lincoln Stein]

I had a look at the output of bigBedSummary, which is from Jim Kent's source
tree (no Perl involved), and it appears that the statistics it provides are
limited to coverage; so I don't think you can do anything with the scores if
you're using BigBed indexing. Have a look at BedGraph=>BigWig and see if it
meets your needs.

Lincoln

On Mon, Jul 4, 2011 at 9:04 AM, Lincoln Stein <lincoln.stein at gmail.com>wrote:

> Hi Dan,
>
> The documentation for BigBed is scanty; all I know about it is what is
> provided by the bigbed library is in Jim Kent's bigbed.h include file. I had
> thought that the scores in BED files would come through into the summary
> statistics like those in BigWig, but now I'm looking at the example data
> provided in Jim's source code, and see that the BigBed example source file
> has scores of "0".
>
> I'll investigate whether there is an issue in the Perl layer, but it could
> easily be a limitation in the library itself. Have you considered using a
> BedGraph file and indexing it with bedGraphToBigWig? I know that the
> Bio::DB::BigWig interface works perfectly to retrieve and summarize the
> scores.
>
> Lincoln
>
>
> On Sun, Jul 3, 2011 at 5:48 AM, Daniel Lang <
> Daniel.Lang at biologie.uni-freiburg.de> wrote:
>
>> Hi,
>>
>> quick question about the BigBed adaptor: Is it correct that the bin and
>> summary functions only return statistics about the number of features in
>> the defined intervals?
>> I was expecting them to deliver statistics about the score if the
>> respective bb file has a defined score field.
>> If this is true, does this also mean that I cannot plot the distribution
>> of scores in BigBed files in gbrowse?
>>
>> This is the first time I'm using BigBed, maybe I'm doing something
>> wrong...
>>
>> I had some trouble formatting the bed files correctly in order to see
>> the score in the features returned by the Bio::DB::BigBed::features()
>> routine. It seems the bigbed entries will only have a correctly assigned
>> score field if you also provide a non-empty name field. Initially I
>> thought that the order of columns is irrelevant if you use an .as file
>> in the bedToBigBed call, but that doesn't seem to be the case.
>>
>> Best,
>> Daniel
>> --
>>
>> Dr. Daniel Lang
>> University of Freiburg, Plant Biotechnology
>> Schaenzlestr. 1, D-79104 Freiburg
>> fax:        +49 761 203 6945
>> phone:      +49 761 203 6989
>> homepage:   http://www.plant-biotech.net/
>>            http://www.cosmoss.org/
>> e-mail <http://www.cosmoss.org/e-mail>:
>> daniel.lang at biologie.uni-freiburg.de
>>
>> #################################################
>> My software never has bugs.
>> It just develops random features.
>> #################################################
>>
>>
>>
>>
>>
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>
>
>
> --
> Lincoln D. Stein
> Director, Informatics and Biocomputing Platform
> Ontario Institute for Cancer Research
> 101 College St., Suite 800
> Toronto, ON, Canada M5G0A3
> 416 673-8514
> Assistant: Renata Musa <Renata.Musa at oicr.on.ca>
>



-- 
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa at oicr.on.ca>