Hi Kyle, Yes, this is likely the problem. hg19.2bit is required anyway for a minimal browser installation for the hg19 assembly. You can rsync the file from here:
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/ Please try using the complete file and let us know if this solves the issue, Thanks, Jennifer --------------------------------- Jennifer Jackson UCSC Genome Informatics Group http://genome.ucsc.edu/ On 6/2/10 10:51 AM, Kyle Tretina wrote: > Hi Jennifer, > > When I loaded the data, I did not alter it; it is intact. As far as the > /gbdb files, snp130.fa was downloaded via rsync from /hg18 and > chr16.2bit was downloaded via ftp as chr16.fa and converted to a .2bit > file using the Blat-package program faToTwoBit. I then created a link to > chr16.2bit called "hg19.2bit". Perhaps this is where my problem is? As > far as the tables, I loaded all of the minimal tables as well as all of > the tables associated with the snp130 track, with no restrictions. > > Thanks, > > Kyle Tretina > Wheaton College > > > > On Tue, Jun 1, 2010 at 11:50 AM, Jennifer Jackson <[email protected] > <mailto:[email protected]>> wrote: > > 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] <mailto:[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] > <mailto:[email protected]> > https://lists.soe.ucsc.edu/mailman/listinfo/genome > > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
