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 <[email protected]> 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 >> [email protected] >> http://lists.bx.psu.edu/listinfo/galaxy-dev >> >> >> >> -- >> Graduate student, Bioinformatics and Genomics >> Makova lab/Galaxy team >> 505 Wartik lab >> University Park PA 16802 >> [email protected] >> > > > > > -- > Graduate student, Bioinformatics and Genomics > Makova lab/Galaxy team > 505 Wartik lab > University Park PA 16802 > [email protected] >
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