If you have the kent utility genePredToGtf, you can convert the UCSC genePred format file directly into the gtf format:
$ mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -N \ -e "select * from ensGene;" mm9 | cut -f2- | genePredToGtf file stdin ensGene.gtf The linux x86_64 version of this binary can be found here: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/ --Hiram sylee wrote: > Dear Sir/Ma'am > > Hi, I downloaded current version of Mus_musculus GTF file from UCSC Tables. > However I have the following problem. > > 1. If I select 'Ensembl Genes' track, the schema for Ensembl Genes has > 'name2'(Gene symbol) column. > But, when I select GTF output format, GTF file doesn't have [gene name2] > column, it has only gene_id(Ens ID) and transcript_id in Attribute column. > like this: > chr1 mm9_ensGene CDS 134222783 134222806 0.000000 > + 2 gene_id "ENSMUST00000072177"; transcript_id > "ENSMUST00000072177"; > > And, when I select 'RefSeq Genes' track and GTF output format, this GTF file > doesn't have name column(NM_number). > Could you let me know how I can get the name2(gene symbol) or refSeq > 'NM_number' in GTF file? _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
