From the public MySQL server directly to Gtf:
mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -N \
-e "select chrom,chromStart,chromEnd,name,score,strand,thickStart,thickEnd from
wgRna;" hg19 \
| bedToGenePred stdin stdout | genePredToGtf file stdin hg19.wgRna.gtf
This will give you a more fully annotated gtf file than the version you obtain
from the table browser.
--Hiram
_______________________________________________
Genome maillist - [email protected]
https://lists.soe.ucsc.edu/mailman/listinfo/genome
