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
