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

[Lincoln Stein]

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
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>
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Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
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