[Genome] Quality scores

[James Taylor]

Hi Kayla,

Is there any way to get the original qa files that were used to  
generate the quality tables in these assemblies? These appear to be  
available for panTro2 [1] but not for most of the assemblies listed  
below. We would prefer not to use the data from the table browser,  
since it has been converted to the lossy "wib" format and we are  
concerned about accumulated error.

Thanks,
James

.. [1]: http://hgdownload.cse.ucsc.edu/goldenPath/panTro2/bigZips/ 
chromQuals.tar.gz

On Oct 8, 2007, at 4:44 PM, Kayla Smith wrote:

>
> Hello Guru,
>
> We have quality scores for some other assemblies.  The table is named
> "quality" in the respective assembly:
>
> anoCar1
> bosTau1
> bosTau2
> bosTau3
> caePb1
> canFam1
> canFam2
> equCab1
> felCat3
> galGal2
> gasAcu1
> monDom1
> monDom4
> oryLat1
> panTro1
> panTro2
> priPac1
> rheMac2
> strPur1
>
> For assemblies which do not have a quality table, you might be  
> interested
> in checking out the PHRED program:
> http://www.phrap.com/phred/
>
> I hope this information is helpful to you.  Please don't hesitate to
> contact us again if you require further assistance.
>
> Kayla Smith
> UCSC Genome Bioinformatics Group
>
> On Mon, 8 Oct 2007, Guruprasad Ananda wrote:
>
>> Hi,
>>
>> I noticed that on the UCSC genome browser, quality score are
>> available for download for chimpanzee and rhesus genomes. I was
>> wondering if you had quality scores for other genomes. If not, could
>> you suggest me an alternative place from where I can obtain quality
>> scores for other genomes?
>>
>> Regards,
>> Guru.
>>
>> Guruprasad Ananda
>> Graduate Student
>> Bioinformatics and Genomics
>> The Pennsylvania State University
>>
>>
>>
>> _______________________________________________
>> Genome maillist  -  Genome at soe.ucsc.edu
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>>
> _______________________________________________
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> http://www.soe.ucsc.edu/mailman/listinfo/genome