Hello, The problem is with the BED file formatting in the data lines (the track line is fine). http://genome.ucsc.edu/FAQ/FAQformat#format1
Specifically, the first column is required to be the chromosome/scaffold name, in exactly the same format as stored in the database. For this genome, it is simply "chr". Reformatting like this (below) will allow the data submission through the Custom track tool: track name=silly_test description="test1" useScore=1 chr 100 200 stupid chr 200 300 more_stupid To find out the formatting of chromsome/scaffold namesfor any assembly, go to the gateway page and click through the "Sequences" link at the top of the second section to view the names and lengths (and sequence data if you click through further). Examining the table "gold" either in the Table browser (when available) or in the file Downloads/Assemby/Annotation Database/ location will also reveal the same information. We hope this helps! Jennifer ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "Francois Heslot" <[email protected]> wrote: > From: "Francois Heslot" <[email protected]> > To: [email protected], "Francois Heslot" <[email protected]> > Sent: Tuesday, January 12, 2010 6:38:12 AM GMT -08:00 US/Canada Pacific > Subject: [Genome] problem with track annotation upload /file format > > Dear Sir, > I am having problem for uploading a mock track-annotation file, for > the > acinetobacter sp ADP1 genome. > * > *I tried to make a mock BED file, following the example given on your > site. > > I wrote this test file (*UCSCtest.txt) *under windows, using WordPad, > > and saved as '.txt' > the data is tab-separated when I typed it. > I have attached the file > it contains 3 lines, shown below: > > track name=silly_test description="test1" useScore=1 > acinSp_ADP1 100 200 stupid > acinSp_ADP1 200 300 more_stupid > > > when uploading the file (file selection / upload), I get: > */Error/ File 'UCSCtest.txt' - Unrecognized format line 2 of custom > track: acinSp_ADP1 100 200 stupid (note: chrom names are case > sensitive) > * > I do not understand what is the problem encountered. > What is going wrong ? > is there a required way to specify that this is to be understood as a > > BED file ? > is the name of the data wrong ? > > thanks, > F. Heslot > ** > > -- > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > Francois HESLOT > > [email protected] > ph (33) 1 4432 2560, or (33) 14432 2566 > fax (33) 1 4432 3840 > > Ecole Normale Superieure, lab LPA > 24 Rue Lhomond > 75005 Paris > FRANCE > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > > track name=silly_test description="test1" useScore=1 > acinSp_ADP1 100 200 stupid 100 > acinSp_ADP1 200 300 more_stupid 100 > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
