Hello Guru,
We have posted the quality score files for the following organisms in
these
locations. They are zipped fasta files.
http://hgdownload.cse.ucsc.edu/goldenPath/bosTau4/bigZips/bosTau4.quals.fa.gz
http://hgdownload.cse.ucsc.edu/goldenPath/calJac1/bigZips/calJac1.quals.fa.gz
http://hgdownload.cse.ucsc.edu/goldenPath/canFam2/bigZips/canFam2.quals.fa.gz
http://hgdownload.cse.ucsc.edu/goldenPath/cavPor3/bigZips/cavPor3.quals.fa.gz
http://hgdownload.cse.ucsc.edu/goldenPath/echTel1/bigZips/echTel1.quals.fa.gz
http://hgdownload.cse.ucsc.edu/goldenPath/equCab1/bigZips/equCab1.quals.fa.gz
http://hgdownload.cse.ucsc.edu/goldenPath/equCab2/bigZips/equCab2.quals.fa.gz
http://hgdownload.cse.ucsc.edu/goldenPath/eriEur1/bigZips/eriEur1.quals.fa.gz
http://hgdownload.cse.ucsc.edu/goldenPath/felCat3/bigZips/felCat3.quals.fa.gz
http://hgdownload.cse.ucsc.edu/goldenPath/galGal3/bigZips/galGal3.quals.fa.gz
http://hgdownload.cse.ucsc.edu/goldenPath/gasAcu1/bigZips/gasAcu1.quals.fa.gz
http://hgdownload.cse.ucsc.edu/goldenPath/monDom4/bigZips/monDom4.quals.fa.gz
http://hgdownload.cse.ucsc.edu/goldenPath/ornAna1/bigZips/ornAna1.quals.fa.gz
http://hgdownload.cse.ucsc.edu/goldenPath/oryCun1/bigZips/oryCun1.quals.fa.gz
http://hgdownload.cse.ucsc.edu/goldenPath/oryLat2/bigZips/oryLat2.quals.fa.gz
http://hgdownload.cse.ucsc.edu/goldenPath/otoGar1/bigZips/otoGar1.quals.fa.gz
http://hgdownload.cse.ucsc.edu/goldenPath/panTro2/bigZips/panTro2.quals.fa.gz
http://hgdownload.cse.ucsc.edu/goldenPath/petMar1/bigZips/petMar1.quals.fa.gz
http://hgdownload.cse.ucsc.edu/goldenPath/rn4/bigZips/rn4.quals.fa.gz
http://hgdownload.cse.ucsc.edu/goldenPath/sorAra1/bigZips/sorAra1.quals.fa.gz
http://hgdownload.cse.ucsc.edu/goldenPath/taeGut1/bigZips/taeGut1.quals.fa.gz
http://hgdownload.cse.ucsc.edu/goldenPath/tupBel1/bigZips/tupBel1.quals.fa.gz
Regards,
----------
Ann Zweig
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu
Jennifer Jackson wrote:
> Hello again,
> The quality files are not already created and cannot be converted from
> the wib files. The fastest solution may be to download the data from the
> original assembly source (as noted in the Source/Credits on each
> assembly Gateway page). We are discussing alternatives.
> Thank you,
> Jennifer
>
> Guruprasad Ananda wrote:
>> Thanks a lot. We are actually working with 36 way alignments, and we
>> would be using qual scores of several more species, which are listed
>> below. Do you think you could provide .qv files for all of them? Or if
>> you could provide us the binary to convert wib to qv, we'll take care
>> of it.
>>
>> bosTau2 ftp://hgdownload.cse.ucsc.edu/gbdb/bosTau2/wib
>> calJac1 ftp://hgdownload.cse.ucsc.edu/gbdb/calJac1/wib
>> canFam2 ftp://hgdownload.cse.ucsc.edu/gbdb/canFam2/wib
>> cavPor3 ftp://hgdownload.cse.ucsc.edu/gbdb/cavPor3/wib
>> danRer5 ftp://hgdownload.cse.ucsc.edu/gbdb/danRer5/wib
>> equCab2 ftp://hgdownload.cse.ucsc.edu/gbdb/equCab2/wib
>> felCat3 ftp://hgdownload.cse.ucsc.edu/gbdb/felCat3/wib
>> fr2 ftp://hgdownload.cse.ucsc.edu/gbdb/fr2/wib
>> galGal3 ftp://hgdownload.cse.ucsc.edu/gbdb/galGal3/wib
>> gasAcu1 ftp://hgdownload.cse.ucsc.edu/gbdb/gasAcu1/wib
>> mm9 ftp://hgdownload.cse.ucsc.edu/gbdb/mm9/wib
>> monDom4 ftp://hgdownload.cse.ucsc.edu/gbdb/monDom4/wib
>> ornAna1 ftp://hgdownload.cse.ucsc.edu/gbdb/ornAna1/wib
>> oryLat2 ftp://hgdownload.cse.ucsc.edu/gbdb/oryLat2/wib
>> rn4 ftp://hgdownload.cse.ucsc.edu/gbdb/rn4/wib
>> taeGut1 ftp://hgdownload.cse.ucsc.edu/gbdb/taeGut1/wib
>> tetNig1 ftp://hgdownload.cse.ucsc.edu/gbdb/tetNig1/wib
>> xenTro2 ftp://hgdownload.cse.ucsc.edu/gbdb/xenTro2/wib
>>
>> Thanks!
>> Guru.
>>
>>
>> On Jun 5, 2009, at 3:59 PM, Jennifer Jackson wrote:
>>
>>> Hello,
>>>
>>> We have added the file to the Downloads location:
>>> ftp: goldenPath/anoCar1/bigZips/anoCar1.qual.qv.gz
>>>
>>> The data is also accessible from the source:
>>> ftp://ftp.broad.mit.edu/pub/assemblies/reptiles/lizard/AnoCar1.0/assembly.quals.gz
>>>
>>>
>>> Thanks,
>>> Jennifer Jackson
>>> UCSC Genome Bioinformatics Group
>>>
>>> Guruprasad Ananda wrote:
>>>> Hi,
>>>>
>>>> I downloaded the anoCar1 qual scores file from ftp://
>>>> hgdownload.cse.ucsc.edu/gbdb/anoCar1/wib, and it is in .wib format.
>>>> I would like to convert this to .qv format which would contain base
>>>> by base qual scores in multiple fasta format (1 fasta per chr).
>>>> Some of your qual score datasets already exist in this format. For
>>>> instance, rheMac2 qual score file at
>>>> http://hgdownload.cse.ucsc.edu/goldenPath/
>>>> rheMac2/bigZips/rheMac2.qual.qv.gz.
>>>> I tried using the hgWiggle binary for this conversion, but in vain.
>>>> Can you please direct me to the right binary for this conversion?
>>>>
>>>> Thanks,
>>>> Guru.
>>>>
>>>> Guruprasad Ananda
>>>> Graduate Student
>>>> Bioinformatics and Genomics
>>>> The Pennsylvania State University
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> Genome maillist - [email protected] <mailto:[email protected]>
>>>> https://lists.soe.ucsc.edu/mailman/listinfo/genome
>>>>
>>>>
>>>>
>> Regards,
>>
>> Guruprasad Ananda
>> Graduate Student
>> Bioinformatics and Genomics
>> The Pennsylvania State University
>>
>>
>>
> _______________________________________________
> Genome maillist - [email protected]
> https://lists.soe.ucsc.edu/mailman/listinfo/genome
_______________________________________________
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