Opened 10 years ago

Closed 10 years ago

Last modified 10 years ago

#1623 closed task (fixed)

Create reporter importer for GTF files

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: critical Milestone: BASE 3.0
Component: coreplugins Version:
Keywords: Cc:

Description

A description of the GTF file format can be found at: http://www.ensembl.org/info/website/upload/gff.html

The importer should use either the "gene_id" or "transcript_id" as the reporter id and also have an option to use a prefix (eg. hg19).

Other reporter annotations should be configurable to use either one of the standard columns or one of the attributes.

We should provide a default configuration using a standard setup.

This is related to #1153.

Change History (4)

comment:1 Changed 10 years ago by Nicklas Nordborg

Owner: changed from everyone to Nicklas Nordborg
Status: newassigned

comment:2 Changed 10 years ago by Nicklas Nordborg

(In [5761]) References #1623: Create reporter importer for GTF files

Column mapping expressions was incorrect. Should be <gene_id> / <transcript_id>.

comment:3 Changed 10 years ago by Nicklas Nordborg

Resolution: fixed
Status: assignedclosed

(In [5759]) Fixes #1623: Create reporter importer for GTF files

comment:4 Changed 10 years ago by Nicklas Nordborg

(In [5770]) References #1623: Create reporter importer for GTF files

The default configuration now uses transcript_id@seqname as the reporter id. We discovered that this is needed to make up a unique id for all entries that we want to track in array design features and raw data.

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