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how to visualize sub-features of sub-features (e.g. stop_codon_read_through features from Web Apollo) #584

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mpoelchau opened this Issue Apr 23, 2015 · 5 comments

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@mpoelchau

mpoelchau commented Apr 23, 2015

Hi everyone,

I'd like to load data derived from Web Apollo output into Jbrowse as a static track. This particular dataset also has stop_codon_read_through features, which are child features of the CDS. I haven't found a way to specify sub-features of sub-features in trackList.json. Is there a way to do this in Jbrowse that replicates the way stop_codon_read_through features are visualized in Web Apollo?

Thanks!

Monica

@cmdcolin

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cmdcolin commented Apr 24, 2015

Good question, this is actually a tricky problem. It's true that the exported GFF3 of WA includes these readthrough's as a subfeature-of-a-subfeature. This causes problems when it is loaded back into JBrowse...

For context, the exon and CDS are both just one-level subfeatures of the mRNA. But with the two-level-subfeatures problem, the stop_codon_read_through is a subfeature of the CDS, and it is never rendered because renderSubfeatures isn't called recursively.

Why is it that WA can render the readthrough stop codons then? It's because it does not consider the stop_codon_read_through as a subfeature-of-a-subfeatures

The easiest way to fix the problem right now is to make the readthrough stop codon a child of the mRNA. Whether we should do this in WA is now up to debate, and might want cross-posting

@childers

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childers commented Apr 24, 2015

Hi Colin,

I agree that adjusting the parent to be the mRNA is the most
straightforward fix, but the resulting features would no longer follow the
way the sequence ontology
http://www.sequenceontology.org/browser/current_svn/term/SO:0000883 models
this relationship. I think you are right that this deserves more
discussion.

Chris

On Fri, Apr 24, 2015 at 11:01 AM, Colin Diesh notifications@github.com
wrote:

Good question, this is actually a tricky problem. It's true that the
exported GFF3 of WA includes these readthrough's as a
subfeature-of-a-subfeature. This causes problems when it is loaded back
into JBrowse...

For context, the exon and CDS are both just one-level subfeatures of the
mRNA. But with the two-level-subfeatures problem, the
stop_codon_read_through is a subfeature of the CDS, and it is never
rendered because renderSubfeatures isn't called recursively.

Why is it that WA can render the readthrough stop codons then? It's
because it does not consider the stop_codon_read_through as a
subfeature-of-a-subfeatures

The easiest way to fix the problem right now is to make the readthrough
stop codon a child of the mRNA. Whether we should do this in WA is now up
to debate, and might want cross-posting


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#584 (comment).

@mpoelchau

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mpoelchau commented Apr 27, 2015

Thanks for the response, Colin! I was hoping to not have to modify the gff3 file (also for the reason that Chris mentions), but that's what we've done in the interim, and it seems to work thanks to Chris adding a new CSS style:
https://apollo.nal.usda.gov/cimlec/jbrowse/?loc=Scaffold2%3A8879186..8879343&tracks=DNA%2CAnnotations%2Cclec_OGS_v1.2&highlight=

@selewis

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selewis commented May 5, 2015

To me this appears to be a bug in JBrowse. We need to talk to Eric about
it. It shouldn't be on us to kludge around a JBrowse issue.

-S

On Mon, Apr 27, 2015 at 10:41 AM, mpoelchau notifications@github.com
wrote:

Thanks for the response, Colin! I was hoping to not have to modify the
gff3 file (also for the reason that Chris mentions), but that's what we've
done in the interim, and it seems to work thanks to Chris adding a new CSS
style:

https://apollo.nal.usda.gov/cimlec/jbrowse/?loc=Scaffold2%3A8879186..8879343&tracks=DNA%2CAnnotations%2Cclec_OGS_v1.2&highlight=


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#584 (comment).

@cmdcolin cmdcolin referenced this issue Jul 29, 2015

Closed

Optimize1 #504

@rbuels rbuels added the bug label Feb 1, 2018

@rbuels rbuels modified the milestones: 1.12.4, 1.13.0 Feb 1, 2018

@rbuels rbuels modified the milestones: 1.13.0, 1.13.1 Mar 14, 2018

@rbuels rbuels closed this in eb718e5 Mar 28, 2018

@mpoelchau

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mpoelchau commented Mar 29, 2018

Thanks, @rbuels!

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