Hi Gundala, One of our developers has put the files you requested (if they were available) at this location:
http://genome-test.cse.ucsc.edu/goldenPath/hg18/pslTmp/ There are 3 categories of files here: 1. $db.pslParts -- we have these for most, but not all, of the desired databases. 2. monDom4.pslChrom -- instead of the little chunks, monDom4 has per-chrom files. 3. alt.$otherAssembly.pslParts -- we don't have pre-chaining alignments for panTro2, mm8, or danRer4. In case alternative assemblies can be used, there are alt.panTro1.pslParts alt.mm9.pslParts alt.danRer5.pslParts I hope these are helpful! -- Brooke Rhead UCSC Genome Bioinformatics Group On 11/07/08 15:33, Gundala Viswanath wrote: > Dear Brooke, > > Thank you so much for your reply. > > The raw blastz pairwise alignment I am looking > for are "hg18" versus these: > > panTro2 > rheMac2 > mm8 > rn4 > canFam2 > equCab1 > bosTau3 > monDom4 > galGal3 > danRer4 > oryLat1 > tetNig1 > fr2 > > > Truly need your help to make those available > for download. All kind of download format are ok with me. > > - Gundala Viswanath > Jakarta - Indonesia > > > > On Sat, Nov 8, 2008 at 8:09 AM, Brooke Rhead <[EMAIL PROTECTED]> wrote: >> Hello Gundala, >> >> In many cases, we do have the gzipped pre-chaining psl alignments, but we >> don't usually make those available for download due to their size. >> >> If you let us know which alignments you are interested in, we might be able >> to make them available to you. >> >> Note that the files will be in job-sized chunks (e.g. 10MB of some hg18 >> chrom vs. 10MB of some canFam2 chrom), not per-chrom like our axtNet or maf >> downloads. >> >> -- >> Brooke Rhead >> UCSC Genome Bioinformatics Group >> >> >> >> On 11/06/08 23:06, Gundala Viswanath wrote: >>> Dear all, >>> >>> Is there a way I can download the raw >>> BlastZ pairwise alignment from UCSC browser? >>> >>> By "raw" I mean, before chaining and netting. >>> >>> - Gundala >>> _______________________________________________ >>> Genome maillist - [email protected] >>> http://www.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
