I'm trying to analyze the SegDup track for CHM13 in the same way I did for hg38: from R.
# connec to database (works)
con <- dbConnect(MySQL(),
user = "genome",
host = "
genome-mysql.soe.ucsc.edu",
dbname = "hs1")
# query table (fails)
df = dbGetQuery(con, "SELECT
*
FROM hub_3671779_sedefSegDups
WHERE chrom = chrom2
AND chromStart < Start2
")
But I get the error
Error in dbSendQuery(conn, statement, ...) :
could not run statement: Table 'hs1.hub_3671779_sedefSegDups' doesn't exist
I got the db name and table name from
(track description) page which matches the "Table Browser" gui, which IS able to query this table.
I also tried "sedefSegDups" as the table name (fails) and "hub_3671779_hs1" as the dbname (fails).
Thanks
Curtis @ UAB.edu