SQL query of T2T-CHM13/hs1 table hub_3671779_sedefSegDups fails

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Rc Hendrickson

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Jun 27, 2024, 6:10:21 PM (5 days ago) Jun 27
to UCSC Genome Browser Public Support
Dear UCSC, 

I'm trying to analyze the SegDup track for CHM13 in the same way I did for hg38: from R. 

My R code for CHM13 is

library(RMySQL)
# 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




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