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

[Daniel Lang]

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:     daniel.lang at biologie.uni-freiburg.de

#################################################
My software never has bugs.
It just develops random features.
#################################################