WormBase/website — Issue #35: #779 tRNAs not always displaying on the Gene Models Track
Author: Paul-Davis
Created: 2012-02-01 13:33:56+00:00
State: open

Reported by Paul Davis 6 minutes ago

Dear Web Team and interested parties.

It seems that we need to tighten up on display of the tRNAs in the genome browser.

Currently there are 2 methods associated with the tRNAs in elegans

tRNA tRNAscan-SE-1.23

and an additional method in Tier II genomes

tRNAscan-SE-1.3

It appears that the gff aggregator for the Gene Models track is missing some of the gff lines because of the method imposing a slightly different gff_source (or feature).

I guess we have 2 options:

1) Move from 3 methods to a single tRNA (possibly 2) and capture the meta data in the object #Evidence

2) Update the aggregator to be more flexible.

Here is an extreme example of a spliced tRNAScan tRNA not being displayed:

http://www.wormbase.org/db/gene/gene?name=WBGene00023072;class=Gene

Note: There is a ncRNA on the opposite strand which does display, so don't get confused.

GFF:

CHROMOSOME_I tRNAscan-SE-1.23 tRNA 6135832 6135915 . + . Transcript "F56F4.t1" ; Gene "WBGene00023072" ;

CHROMOSOME_I tRNAscan-SE-1.23 intron 6135869 6135879 . + . Transcript "F56F4.t1"

CHROMOSOME_I tRNAscan-SE-1.23 exon 6135832 6135868 . + . Transcript "F56F4.t1"

CHROMOSOME_I tRNAscan-SE-1.23 exon 6135880 6135915 . + . Transcript "F56F4.t1"

Cheers

Paul