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

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Graduate student, Bioinformatics and Genomics

Makova lab/Galaxy team
505 Wartik lab
University Park PA 16802
guru@psu.edu