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
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