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6.1 years ago
gsk1185
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20
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.
Could you show us the bioMart code? Probably with small modifications it is possible to get what you want.
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
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
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