To whom it may concern, So I have run the minimal browser installation using the scripts that you mentioned, and re-loaded the associated tables and I am still receiving the same error when I run a search for an rsnumber on my mirror. This is something to the effect of "Error: expected fasta header, got this line - (some combination of bases) at offset (some number) in file /gbdb/hg18/snp/snp130.fa". I have been stuck with this issue for a little while now I would appreciate any help to be able to view the alignments.
Thanks, Kyle Tretina Wheaton College On Fri, May 14, 2010 at 4:23 PM, Hiram Clawson <[email protected]> wrote: > Good Afternoon Kyle: > > What you probably want to do is run a minimal browser installation > for the genome you want to work with. A minimal browser only > needs about six database tables to get started with and a couple > of files in /gbdb/ > > Note the scripts in the source tree: > src/product/scripts/fetchMinimalGbdb.sh > src/product/scripts/fetchMinimalGoldenPath.sh > which can fetch just the files needed for a minimal browser. > > See also: > http://genomewiki.ucsc.edu/index.php/Minimal_Browser_Installation > > --Hiram > > > Kyle Tretina wrote: > >> To whom it may concern, >> >> There was one area that was a little unclear in the documentation when >> creating a mirror for your site. I am only trying to re-produce the >> alignments for the track SNP(130). The data for gbdb, which I have >> re-downloaded twice and checked the file size for are: >> >> >> /gbdb/hg18/snp/snp130.fa >> >> Also, under a link that Jennifer said would give us direction for building >> a >> chr16 only database ( >> http://genomewiki.ucsc.edu/index.php/Building_a_new_genome_database), I >> followed the instructions but was not sure what parts should be included >> because the page seems to be about a broader topic. >> >> What I did: >> -Download chr16.fa from >> ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/chromosomes/ >> -Convert chr16.fa to chr16.2bit using the BLAT-related program faToTwoBit >> (faToTwoBit chr16.fa chr16.2bit) >> -Move chr16.2bit to the gbdb/hg19 area and create a link to it called >> "hg19.2bit" >> >> I did not continue on with these instructions because it did not seem >> appropriate to what I was doing (for example, I already loaded the gold >> and >> gap tables from another step on the mirror procedures page). Am I missing >> something here? >> >> >> Kyle Tretina >> Wheaton College >> > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
