Hi Rochak,
Rochak Neupane wrote:
Hi,
I am trying to get gff output on a local install of biomart. Seems like an exportable named "gtf" must be defined with a set of attributes.
Copied the following from http://www.biomart.org/biomart/martservice?type=configuration&dataset=oanatinus_gene_ensembl <http://www.biomart.org/biomart/martservice?type=configuration&dataset=oanatinus_gene_ensembl>
<Exportable
attributes="ensembl_gene_id,ensembl_transcript_id,ensembl_exon_id,chromosome_name,exon_chrom_start,exon_chrom_end,coding_start_offset,coding_end_offset,strand,exon_id,rank,start_exon_id,end_exon_id,transcript_count"
internalName="gtf"
linkName="gtf"
name="gtf"
orderBy="ensembl_gene_id,ensembl_transcript_id,rank"
pointer="true"
type="formatter" />
Without having a "gtf" exportable, when I select "GFF" as output type, I get "No attributes selected". When I defined the exportable, no errors, but no output either.
Figured I didn't have proper attributes exported. Could anyone help me with what the required attributes are or rather what they might mean for the gff formatter?
In particular the follwing attributes exported in "gtf":
coding_start_offset --> seq_start_1068 (corresponding field in
__translation__main table in ensembl_mart_54.)
the offset of coding start from the start of the first coding exon
coding_end_offset ----> seq_end_1068
the offset of coding end from the start of the last coding exon
start_exon_id --------> start_exon_id
the id of the first coding exon
end_exon_id ----------> end_exon_id
the id of the last coding exon
Ensembl do not store the coordinates of GFF in the mart anymore, hence
calculations on the fly are needed. If you have the coordinates ready
which correspond to the old gff exportable (ensembl mart 48 and prior) -
use that signature, should work with GFF formatter just fine.
In case, you have a totally different format of storing GFF coordinates
in mart, please, feel free to write your own formatter under
biomart-perl/lib/Formatters/ following similar conventions as in GFF.pm
Hope this helps,
Best,
Syed
Thanks,
Rochak
