Thank you for your answer, it helped. -- Carlos Borroto Baltimore, MD
On Fri, Apr 8, 2011 at 12:02 PM, Vanessa Kirkup Swing <[email protected]> wrote: > 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
