Hello Prashanti, We have a number of gene prediction tracks - you can see them if you go to the medaka browser and scroll down to the "Genes and Gene Prediction Tracks" section. To see the description for any of these tracks you can click on the track title above its configuration pulldown menu. You will have to determine which track best suits your purposes. For each track you can also see the count of how many genes are in the set by looking at the row count for the table housing the data behind that track. To see how many rows (i.e. items/genes/transcripts) click on the "View table schema" link near the top of its description page. You can also use this link to find the table name to use in the Table Browser to retrieve the track data (see below).
The RefSeq track in particular is pulled from NCBI so if you are interested in NCBI data this may be of interest to you. You will find its description page here: http://genome.ucsc.edu/cgi-bin/hgTrackUi?&c=chr2&g=refGene and you can download the table underlying the refseq track here (see the mrna.fa.gz file): http://hgdownload.cse.ucsc.edu/goldenPath/oryLat2/bigZips/ or by selecting that table from the table browser here: http://genome.ucsc.edu/cgi-bin/hgTables Best regards, Pauline Fujita UCSC Genome Bioinformatics Group http://genome.ucsc.edu On 7/10/12 1:36 PM, Prashanti Manda wrote: > Hello, > I am trying to find genes for Medaka sequences. I tried downloading the > relevant databases from > ftp://hgdownload.cse.ucsc.edu/goldenPath/oryLat2/database/ but I am not > sure I am downloading the right data. I looked at > ensGene.txt.gz<ftp://hgdownload.cse.ucsc.edu/goldenPath/oryLat2/database/ensGene.txt.gz>and > geneName.txt.gz<ftp://hgdownload.cse.ucsc.edu/goldenPath/oryLat2/database/geneName.txt.gz>. > When I search for Medaka on the Nucleotide database at NCBI, I get about > 50000 results with gene names. Could you please let me know which tables I > am supposed to be using ? > > Thanks so much for your help. I really appreciate it. > > Regards, > Prashanti > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
