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

[Daniel Lang]

Hi Timothy,

thanks for your immediate and thorough response! That helps me a lot!
I'll try it out directly.

I didn't correctly connect the dots with BigWig vs BigBed. So if I don't
want to identify individual features, I should better use that...

Best,
Daniel


Am 03.07.2011 22:10, schrieb Timothy Parnell:
> Hi Daniel,
> 
> You are correct about the bin and summary function of the BigBed adaptor
> working only with the number of features and not the individual scores.
> 
> There is a workaround, albeit not as efficient as the statistical method.
> In the conf stanza, you'll need to use the region feature, and then use
> the older xyplot glyph. This glyph will iterate through all the bed
> features, calling the score method on each, and then draw an xyplot with
> those collected scores. Be sure to set the group_on function to tie them
> all into one graph. Here is an example.
> 
> [bigbed_score_graph]
> database     = bigbed_db
> feature      = region
> glyph        = xyplot
> graph_type   = line
> group_on     = type
> 
> As for the BED format, per the format definition from UCSC, the first
> three columns (chromosome, start, stop) are required, and any additional
> higher number columns must have the lower columns filled. So to include a
> score (5th column), you need to also fill the name (4th) column.
> 
> If your features don't have names, then I would recommend using the BigWig
> format instead. You can load a bedgraph file (chromosome, start, stop,
> score) into a BigWig database. You'll also have access to the fast summary
> statistical functions that work on the scores.
> 
> Hope that helps.
> Tim
> 
> 
> 
> On 7/3/11 3:48 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:     daniel.lang at biologie.uni-freiburg.de
>>
>> #################################################
>> My software never has bugs.
>> It just develops random features.
>> #################################################
>>
>>
>>
>>
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> 

-- 

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.
#################################################