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
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 _______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
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?
David
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 _______________________________________________ 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 guru@psu.edu
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.govwrote:
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 guru@psu.edu
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 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 _______________________________________________ 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 guru@psu.edu
-- Graduate student, Bioinformatics and Genomics Makova lab/Galaxy team 505 Wartik lab University Park PA 16802 guru@psu.edu
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.govwrote:
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 guru@psu.edu
-- Graduate student, Bioinformatics and Genomics Makova lab/Galaxy team 505 Wartik lab University Park PA 16802 guru@psu.edu
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