[Genome] refGene and refSeqAli table dumps

[Brooke Rhead]

Hello Brian,

You are looking in the correct place for the table dumps.  However, 
there was a recent glitch on our downloads server that prevented these 
tables from getting dumped.  They should reappear in the next several 
days.  In the meantime, you can dump them from the Table Browser by 
selecting each table and choosing "region: genome" and "output format: 
all fields from selected table".  Be sure to enter a name for the output 
file to save it to your computer, and choose the option to compress it 
to speed up the download.

Regarding the difference between refGene and refSeqAli: refSeqAli is 
generated first.  It contains alignment information from BLATing the 
RefSeq sequences against the genome.  The table is in PSL format, 
described here: http://genome.ucsc.edu/FAQ/FAQformat#format2 .  This 
table is used to display the alignments in the "mRNA/Genomic Alignments" 
section of the RefSeq Genes details pages.

The refGene table is generated from refSeqAli and additional information 
from the GenBank record, like where the coding sequence begins and ends, 
and the gene symbol.  It is in the same format as our other gene 
prediction tables.  The information in refGene is used to display the 
RefSeq Genes in the Genome Browser.

I hope this information helps.  If you have further questions, please do 
not hesitate to contact us again.

--
Brooke Rhead
UCSC Genome Bioinformatics Group



Brian O'Connor wrote:
> Hi,
> 
> I'm trying to find the table dumps for the refGene and refSeqAli tables 
> in hg18.  I see them in the table browser 
> (http://genome.ucsc.edu/cgi-bin/hgTables?command=start). However, when I 
> tried looking for them in 
> http://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/ I couldn't find 
> them.  Maybe I'm looking in the wrong place?
> 
> Also, could you clarify the difference in these two tables?
> 
> Thanks very much for your help!!
> 
> --Brian O'Connor
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
> http://www.soe.ucsc.edu/mailman/listinfo/genome