And, exactly what file(s) do you get from UCSC?  I can find some for various 
organisms (goldenPath/[org]/bigZips/[org].quals.fa.gz), but hg18, hg19, mm8, 
and mm9 are not among them.

David

On Feb 1, 2011, at 3:57 PM, Guru Ananda wrote:

> I've successfully installed bx-python, and there are mountain of utility 
> scripts.  Which ones do you use for converting the quals.fa file to binned 
> array format?
> 
>  bx-python/scripts/qv_to_bqv.py
>  
> 
> 
> On Feb 1, 2011, at 2:50 PM, Guru Ananda wrote:
> 
>> Hi David,
>> 
>> We download quality score files (qual.fa) from UCSC and convert them to 
>> binned array format using scripts from bx-python 
>> (https://bitbucket.org/james_taylor/bx-python/wiki/Home) to enable fast 
>> seek. 
>> If you interested in the particulars (which script etc.), please let me know 
>> and I can provide you with the details.
>> 
>> Thanks,
>> Guru.
>> 
>> On Tue, Feb 1, 2011 at 1:23 PM, David Hoover <hoove...@helix.nih.gov> wrote:
>> Where do the files in quality_scores.loc come from?  Can they be downloaded 
>> from UCSC or somewhere else?
>> 
>> David Hoover
>> Helix Systems Staff
>> http://helix.nih.gov
>> _______________________________________________
>> galaxy-dev mailing list
>> galaxy-dev@lists.bx.psu.edu
>> http://lists.bx.psu.edu/listinfo/galaxy-dev
>> 
>> 
>> 
>> -- 
>> Graduate student, Bioinformatics and Genomics
>> Makova lab/Galaxy team
>> 505 Wartik lab
>> University Park PA 16802
>> g...@psu.edu
>> 
> 
> 
> 
> 
> -- 
> Graduate student, Bioinformatics and Genomics
> Makova lab/Galaxy team
> 505 Wartik lab
> University Park PA 16802
> g...@psu.edu
> 

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