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
