>
> 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
>
> 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
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 p
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 moun
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 conver
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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