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.

UCSC doesn't host quality scores for hg18/hg19 since the sequence quality of these assemblies is very high. Perhaps its the same case with mm8/mm9 as well (please check with UCSC). Also, if you're unable to find quality scores of any specific genomes, please write to UCSC mailing list requesting the same.
 


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 <hooverdm@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
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--
Graduate student, Bioinformatics and Genomics
Makova lab/Galaxy team
505 Wartik lab
University Park PA 16802
guru@psu.edu





--
Graduate student, Bioinformatics and Genomics
Makova lab/Galaxy team
505 Wartik lab
University Park PA 16802
guru@psu.edu





--
Graduate student, Bioinformatics and Genomics
Makova lab/Galaxy team
505 Wartik lab
University Park PA 16802
guru@psu.edu