Question: Exons Numbers associated with each gene
1
gravatar for gsk1185
9 months ago by
gsk118520
gsk118520 wrote:

How can I download Exons coordinates & exon Numbers associated with each gene for only one transcript per Gene?I know there are many transcript per Gene. have tried biomart & Table browser but it gives me result for all the transcript.

next-gen gene genome • 324 views
ADD COMMENTlink modified 9 months ago • written 9 months ago by gsk118520
2

Could you show us the bioMart code? Probably with small modifications it is possible to get what you want.

ADD REPLYlink written 9 months ago by h.mon22k

http://grch37.ensembl.org/biomart/martview/b16167edebe773e37076a55ffd569ee0?VIRTUALSCHEMANAME=default&ATTRIBUTES=hsapiens_gene_ensembl.default.structure.ensembl_gene_id|hsapiens_gene_ensembl.default.structure.ensembl_transcript_id|hsapiens_gene_ensembl.default.structure.external_gene_name|hsapiens_gene_ensembl.default.structure.exon_chrom_start|hsapiens_gene_ensembl.default.structure.exon_chrom_end|hsapiens_gene_ensembl.default.structure.is_constitutive|hsapiens_gene_ensembl.default.structure.rank|hsapiens_gene_ensembl.default.structure.phase|hsapiens_gene_ensembl.default.structure.end_phase|hsapiens_gene_ensembl.default.structure.cdna_coding_start|hsapiens_gene_ensembl.default.structure.cdna_coding_end|hsapiens_gene_ensembl.default.structure.genomic_coding_start|hsapiens_gene_ensembl.default.structure.genomic_coding_end|hsapiens_gene_ensembl.default.structure.ensembl_exon_id|hsapiens_gene_ensembl.default.structure.cds_start|hsapiens_gene_ensembl.default.structure.cds_end&FILTERS=&VISIBLEPANEL=resultspanel

ADD REPLYlink written 9 months ago by gsk118520
2

Hello,

and which transcript do you expect for each gene? One solution might be using Ensembl's REST-API. With the lookup endpoint you can get first all exon informations for all your genes. You can than filter your result for e.g. the transcript which is set as "canonical".

fin swimmer

ADD REPLYlink written 9 months ago by finswimmer8.2k

Yes finswimmer i am looking for canonical transcript only. Is it possible in Biomart?? i will also try to install Ensembl's REST-API but it seems to have lot of dependencies. Thanks

ADD REPLYlink modified 9 months ago • written 9 months ago by gsk118520
1
gravatar for gsk1185
9 months ago by
gsk118520
gsk118520 wrote:

Thank you All. I think i have found solution. https://groups.google.com/a/soe.ucsc.edu/forum/#!msg/genome/_6asF5KciPc/VTm611kJHAAJ

ADD COMMENTlink written 9 months ago by gsk118520
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