Good Morning Christian: The gnfAtlas2 table is not a wiggle table. If there is a column of data in that table that you would like to use, simple cut out that column from the file for the values, or select that column from the database table.
hgWiggle only works on wiggle types of tables. --Hiram [email protected] wrote: > Hi, > > I'm using the hgWiggle command for retrieving conservation scores from > our local copy of the genome browser. Which works perfectly. > (hgWiggle -rawDataOut -position=chr9:70840164-70878772 -db=hg18 > phastCons44way;) > > Now I also wanted to use this to get expression data out of the database > so I simply tried: hgWiggle -rawDataOut -position=chr9:70840164-70878772 > -db=hg18 gnfAtlas2; > > However this does not seem to work very well as I get the error : > > Can't start query: > select * from gnfAtlas2 where (bin=1125 or bin=140 or bin=17 or bin=2 or > bin=0 or bin=4681 ) and (chrom = "chr9" AND chromStart < "70878772" AND > chromEnd > "70840163") order by span ASC, chromStart ASC > > It looks like the order by span column is not working because the > gnfAtlas2 table (as opposed to the conservation tables) has no span > column. I noted that at least for the phastCons44way table, the value in > the span column is always 1. > > Is there a way to fix this problem? (I was thinking of maybe adding a > span column to the table, but I'm not sure whether that will mess up > some of the genome browser functionality? Furthermore if I wanted data > from another table I might have to do the same and it will also cause > problems with our updates. ) > > But maybe I'm using the wrong method to extract this data out of the > database? And should I maybe use plain SQL instead? > > Thanks for your help, > > Christian Gilissen > Department of Human Genetics > Radboud University Nijmegen Medical Center > Nijmegen, the Netherlands > > > > > > > > > Het UMC St Radboud staat geregistreerd bij de Kamer van Koophandel in het > handelsregister onder nummer 41055629. > The Radboud University Nijmegen Medical Centre is listed in the Commercial > Register of the Chamber of Commerce under file number 41055629. > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
