Hi Motokazu,
Sorry for the delay in answering this - somehow we missed it.
Do you still need help with this? If so can you supply the command-line
usage?
best wishes
Ian
Motokazu Ishikawa wrote:
> I want to show exon-intron strucutre of mRNA. mRNA shape (gray arrow)
> can successfully be shown, but subfeatures (UTR and CDS) weren't shown
> on on it. Any subfeature-*.json file weren't created under data/tracks
> directory. Could you give me some advices ?
>
> GFF3 file and config file are belows.
>
> ** GFF3 file
>
> chr22 hg18_refGene gene 49288242 49293001 . - . ID=gene:NM_033200;
> Name=gene:NM_033200;Note=NM_033200
> chr22 hg18_refGene mRNA 49288242 49293001 . - . ID=mRNA:NM_033200.1;
> Name=mRNA:NM_033200.1; Parent=gene:NM_033200; Index=1
> chr22 hg18_refGene five_prime_UTR 49292971 49293001 . - .
> ID=five_prime_UTR:NM_033200.1.1; Name=five_prime_UTR:NM_033200.1.1;
> Parent=mRNA:NM_033200.1
> chr22 hg18_refGene CDS 49292877 49292970 . - 0 ID=CDS:NM_033200.1.2;
> Name=CDS:NM_033200.1.2; Parent=mRNA:NM_033200.1
>
>
> ** conf file
>
> {
> "description": "ucsc tracks",
> "db_adaptor": "Bio::DB::SeqFeature::Store",
> "db_args": { "-adaptor": "memory",
> "-dir": "stage/ucsc" },
> "TRACK DEFAULTS": {
> "class": "feature",
> "autocomplete": "all"
> },
> "tracks": [
> {
> "track": "ucsc_gene",
> "key": "ucsc Gene Span",
> "feature": ["gene"],
> "autocomplete": "all",
> "class": "feature2",
> "category": "Gene Model features",
> "urlTemplate": "http://flybase.org/cgi-bin/fbidq.html?{load_id}",
> "extraData": {"load_id": "sub {shift->attributes(\"load_id\");}"}
> },
> {
> "track": "ucsc_mRNA",
> "feature": ["mRNA"],
> "autocomplete": "alias",
> "subfeatures": true,
> "key": "ucsc mRNA",
> "class": "transcript",
> "subfeature_classes": {
> "CDS": "transcript-CDS",
> "five_prime_UTR": "transcript-five_prime_UTR",
> "three_prime_UTR": "transcript-three_prime_UTR"
> },
> "arrowheadClass": "transcript-arrowhead",
> "clientConfig": {
> "histScale":5
> },
> "urlTemplate":
> "http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=search&term={load_id}",
> "extraData": {"load_id": "sub {shift->attributes(\"load_id\");}"}
> },
> {
> "track": "ucsc_snp",
> "feature": ["point_mutation"],
> "key": "ucsc Mutation: point mutation",
> "class": "feature",
> "category": "Mapped features"
> }
> ]
> }
>
>
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