WormBase/website — Issue #54: GBrowse track additions
Author: tharris
Created: 2012-02-07 14:19:55+00:00
State: open
Labels: gbrowse, user interface

Sanger has produced a number of new feature types over the last few months, so I need to start their integration into the visible parts of WormBase.org.

Would it be possible to get 4 new tracks added to the misc section of GB2 (& GB1 if we are still using it anywhere?)?

I guess I need to give you a description and example GFF?

These would be:

Genome_sequence_error - A position within the genome that has been identified as having a base call error when compared to a 3rd party sequence data. The error state (Corrected or Not) and the exact change can be establised by looking in the individual features.

CHROMOSOME_II.gff:CHROMOSOME_II	RNASeq	possible_base_call_error	5435677	5435679	.	-	.	Feature "WBsf047691"

segmental_duplication - Polymorphic segmental duplication as defined by the tool OrthoCluster. This feature represents one sequence from a pair of duplicons in the N2 genome.

CHROMOSOME_X	segmental_duplication	segmental_duplication	17459144	17460071.+	.	Feature "WBsf042126"

transcription_start_site - transcription_start_site defined by analysis of RNASeq short read datasets (example Hillier et al.)

CHROMOSOME_II.gff:CHROMOSOME_II	RNASeq	transcription_start_site	5435677	5435679	.	-	.	Feature "WBsf063234"

transcription_end_site - transcription_end_site defined by analysis of RNASeq short read datasets (example Hillier et al.)

CHROMOSOME_II.gff:CHROMOSOME_II	RNASeq	transcription_end_site	5435677	5435679	.	-	.	Feature "WBsf063234"

Not all of these will be available in the gff immediately, but will be coming in the next couple of releases.

Thanks

Paul

Edit Spam Delete
Status:	open	Responsible:	Abigail Cabunoc	Type:	enhancement	Priority:	major
Milestone:	none	Component:	GBrowse	Version:	WS222
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Comments and changes
#1Paul Davis
written 2010-04-21
Changed content.
#2Todd Harris
written 2010-04-28
Changed status from new to open.
Changed responsible from tharris to acabunoc.
Changed version from WS214 to WS215.
#3Todd Harris
written 2010-09-17
Changed component from Classic WormBase to GBrowse.
#4Paul Davis
written 2011-01-26, last edited 2011-01-26
Changed version from WS215 to WS222.
Hi,

I have another new addition to the track list.

Could I get a Transposon track added?

GFF:

CHROMOSOME_I	Transposon	transposable_element	11338202	11339445	.	-	.	Transposon "WBTransposon00000298"
CHROMOSOME_I	Transposon	transposable_element	11426824	11427473	.	-	.	Transposon "WBTransposon00000202"
CHROMOSOME_I	Transposon	transposable_element	11849268	11851604	.	-	.	Transposon "WBTransposon00000066"
CHROMOSOME_I	Transposon	transposable_element	11943129	11944372	.	-	.	Transposon "WBTransposon00000299"
Track help/ description:

These are Transposon markups that have been reviewed by WormBase curators.
I guess it would be good if you could get a rudimentary summary page if you clicked on them in GB2?

Information on page would be

ID: WBTransposon0000000001
Species
Type (Taken from Member_of tag)
Copy_status
Remark
link to the genome browser.
Thanks

Paul