Hi Carlos, You are missing the linkage of tables. The knownGenes table has about 50 related tables and there is code for this track makes this track very unique. It sounds like you want a subset of knownGenes to display? There isn't a way to get exactly the format that you are looking for, but one option would be to create a custom track by pasting in the list of knownGenes you want to study using the table browser (http://genome.ucsc.edu/cgi-bin/hgTables) and have that track display above or below GTF track that you have created.
If you have questions on how to do this, please don't hesitate in contacting the mailing list: [email protected] Vanessa Kirkup Swing UCSC Genome Bioinformatic Group ----- Original Message ----- From: "Carlos Javier Borroto" <[email protected]> To: "genome" <[email protected]> Sent: Thursday, April 7, 2011 10:26:50 AM Subject: [Genome] How to make local tracks from GTFs to look more like knownGene track? Hi, I have GTF files I display in a local mirror, I would like to have configuration options like which label to show("gene symbol", "UCSC Known Gene ID", etc), I looked into kent/src/hg/makeDb/trackDb/trackDb.ra and I see this configuration for that track: track knownGene shortLabel UCSC Genes longLabel UCSC Genes Based on RefSeq, UniProt, GenBank, CCDS and Comparative Genomics group genes priority 34 visibility pack color 12,12,120 type genePred knownGenePep knownGeneMrna idXref kgAlias kgID alias hgGene on hgsid on directUrl /cgi-bin/hgGene?hgg_gene=%s&hgg_chrom=%s&hgg_start=%d&hgg_end=%d&hgg_type=%s&db=%s baseColorUseCds given baseColorDefault genomicCodons defaultLinkedTables kgXref intronGap 12 I read most options explanations from kent/src/hg/makeDb/trackDb/README and copy some of them to my local track, but still couldn't made it to work. I'm loading my GTF files with ldHgGene. Part of my GTF file: chr1 Cufflinks transcript 11874 14409 1 + . gene_id "uc010nxq.1"; transcript_id "uc010nxq.1"; FPKM "0.0000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "0.000000"; chr1 Cufflinks exon 11874 12227 1 + . gene_id "uc010nxq.1"; transcript_id "uc010nxq.1"; exon_number "1"; FPKM "0.0000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "0.000000"; chr1 Cufflinks exon 12595 12721 1 + . gene_id "uc010nxq.1"; transcript_id "uc010nxq.1"; exon_number "2"; FPKM "0.0000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "0.000000"; chr1 Cufflinks exon 13403 14409 1 + . gene_id "uc010nxq.1"; transcript_id "uc010nxq.1"; exon_number "3"; FPKM "0.0000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "0.000000"; How I load the GTF file info: ldHgGene -genePredExt hg19 NRM02DEV_GAIIx_KNOWN_TRANSCRIPTS KNOWN/Hg19_NRM2_GAII.known.transcripts.gtf My current track configuration: track NRM02DEV_GAIIx_KNOWN_TRANSCRIPTS superTrack NRMDEV full shortLabel NRM02DEV known transcripts longLabel GAIIx NRM02DEV known transcripts type genePred priority 5.013 idXref kgAlias kgID alias hgGene on hgsid on defaultLinkedTables kgXref I guess I'm missing the actual linking of the tables, maybe something else have to be done. Any help would be highly appreciated, Thanks, -- Carlos Borroto Baltimore, MD _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
