Hi Kyle, Very sorry to hear this procedure is still causing you problems. Let's try to get it working.
When you loaded the data (tables and /gbdb files), did you alter it to restrict it to your chromosome of interest (chr16)? Or did you leave everything intact (safest method)? It would probably be OK to limit to chr16 in the mySQL loaded table(s) if you really need/want to, but do not alter the snp130.fa file in /gbdb. If you do alter the /gbdb file, then the pointers in the snp tables will not function correctly to retrieve data, which sounds the problem. And to double check: all of the files are from the same download/release cycle? Please let us know about the snp files/tables and we can follow up from there, Thank you, Jennifer --------------------------------- Jennifer Jackson UCSC Genome Informatics Group http://genome.ucsc.edu/ On 6/1/10 7:53 AM, Kyle Tretina wrote: > 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 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
