Hello, The Table browser currently supports GTF format. The format GFF3 is very similar to GTF. GTF is the original name assigned to GFF version 2. It sounds complicated, but in practical terms, GFF3 is backward-compatible with GTF according to online documentation plus there are validation programs that you can use to confirm this once you have the data (google GFF3 for the alternatives).
Links to the data specs at the UCSC Browser site: GTF http://genome.ucsc.edu/FAQ/FAQformat#format4 To extract data for human genes in GTF format from the Table browser http://genome.ucsc.edu/cgi-bin/hgTables 1) Set the clade, genome, assembly to the appropriate genomic version 2) Set group = "Gene and Gene Prediction Tracks" 3) Set the track. Start with UCSC Genes or RefSeq and try others as desired. Read the track description, contents, methods, credits, etc. by clicking on "describe table schema" for the default table and scroll to bottom of page. Or, open the Assembly browser and click on the track names. 4) For all data, set region = genome and leave the remaining values as default. 5) Set output format = GTF (gene transfer format), name output file, and "get output" to download. Table browser help and tutorial links are in the top paragraph of the form. If you need additional help, please let us know, Jennifer Jackson UCSC Genome Bioinformatics Group joseph wrote: > Hi > Can you please show me how to download a GFF3 file for the annotation of > human genes? > Thanks > Joseph > > > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
