Hello, The GFF format specifies that the first column of data must be: "seqname - The name of the sequence. Must be a chromosome or scaffold." Meaning, a base chromosome or scaffold in the target assembly. Here is the GFF format FAQ http://genome.ucsc.edu/FAQ/FAQformat#format3
Lines will fail to load when the first column is not an exact name match for one of the 14 base chromosomes in this target assembly. From the example, it looks as if you have "apidb|chr1" instead of "chr1". This is where your load failed - on the first line of uncommented content with seqname formatted differently than expected. As a test, using just chr1 and following the seqname rules, I took the first full chr1 line plus the first 3 lines representing data on chr1 and altered them. I also double checked that I had tabs between the data columns (important). The load worked. track name=test description="Test GFF" chr1 ApiDB supercontig 1 643292 . + . ID=apidb|MAL1;Name=MAL1;description=MAL1;size=643292;web_id=MAL1;molecule_type=dsDNA;organism_name=Plasmodium falciparum;translation_table=11;topology=linear;localization=nuclear;Dbxref=ApiDB_PlasmoDB:MAL1,GenBank:NC_004325,taxon:36329 chr1 ApiDB gene 474888 477036 . + . ID=apidb|MAL1_18s;Name=MAL1_18s;description=18s+rRNA+A-type;size=2149;web_id=MAL1_18s;locus_tag=MAL1_18s;size=2149 chr1 ApiDB rRNA 474888 477036 . + . ID=apidb|rna_MAL1_18s-1;Name=MAL1_18s-1;description=18s+rRNA+A-type;size=2149;Parent=apidb|MAL1_18s;Dbxref=ApiDB_PlasmoDB:MAL1_18s,Sanger:MAL1_18s,taxon:36329 chr1 ApiDB exon 474888 477036 . + . ID=apidb|exon_MAL1_18s-1;Name=exon;description=exon;size=2149;Parent=apidb|rna_MAL1_18s-1 Try this formatting change and let us know if you continue to have problems. Some other help for this particular browser should you have content questions/comments: contact info: [email protected] comment form: http://areslab.ucsc.edu/browserusercomments.html Jennifer Jackson UCSC Genome Bioinformatics Group Wonjong Moon wrote: > Hello, I was trying to upload custrom track gff file to P. falciparum > (Plasmodium falciparum) Genome Browser Gateway > http://areslab.ucsc.edu/cgi-bin/hgCustom > > I want to use newer P.falciparum sequence file. > > I downloaded this p.falciparum 5.5 gff file from > http://plasmodb.org/common/downloads/release-5.5/Pfalciparum/Pfalciparum > _PlasmoDB-5.5.gff > And changed MAL1 to chr1, MAL2 to chr2, and so on. > I uploaded the gff file to to P. falciparum (Plasmodium falciparum) > Genome Browser Gateway, but got an error. > > Error File 'Pfalciparum_PlasmoDB-5.5chr.gff' - Unrecognized format > line 24 of custom track: apidb|chr1 ApiDB supercontig 1 643292 . + . > ID=apidb|chr1;Name=chr1;description=chr1;size=643292;web_id=chr1;molecul > e_type=dsDNA;organism_name=Plasmodium > falciparum;translation_table=11;topology=linear;localization=nuclear;Dbx > ref=ApiDB_PlasmoDB:chr1,GenBank:NC_004325,taxon:36329 (note: chrom names > are case sensitive) > > Unmodified gff file also got the same error message. > > Is it possible to use P.falciparum gff file with > http://areslab.ucsc.edu/cgi-bin/hgCustom ? Or should I install a local > genome browser and customize it? > > Thanks, > > Wonjong. > > SBRI. > _______________________________________________ > Genome maillist - [email protected] > http://www.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
