[Gmod-ajax] FeatureSequence Viewer Weridness

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[Gmod-ajax] FeatureSequence Viewer Weridness

Sofia Robb
Most of the time I can get the viewer to display only the CDS sequence just fine, but occasionally I find that it does not. But it does highlight appropriately.

This might be because of the overlapping subfeatures, but I get errors about overlapping subfeatures for every transcript I have selected, most of which result in good sequence.

here is the error i get for the transcript for which I cannot get only the CDS sequence to display (but like I said, the appropriate CDS sequence can highlighted)

Warning: Overlap between features: exon_13 and CDS_14
Overlapping subfeatures will cause problems in viewing their boundaries.
This may also cause the Feature Sequence Viewer to respond slowly. 


to view only the CDS, I "Hide" all the subfeatures, then "Show" the CDSs. As you can see more than just the CDS (highlighted) is being dsiplayed

Inline image 1

What is interesting, is that when I hide all the subfeatures, there is still sequence displayed. I also noticed that there is no "other" subfeature listed.

Inline image 2


Thanks,
Sofia

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Re: FeatureSequence Viewer Weridness

Saari, Travis

Hi Sofia,

 

This is likely because the CDS and the exon in this case do not overlap perfectly. In the other cases, I’m guessing you don’t see any issues because the CDS and exons overlap perfectly. Can you check the annotation file and see if this is the case? I’ve recently discovered that the GFF3 specification implies UTRs as exon regions without CDS overlap. Perhaps this is what’s going on with the annotation.

 

I have plans to make the FeatureSequence plugin “smarter”, so that it can better handle the common case of a gene-> mRNA -> CDS/exon structure found in most annotations, and follow the GFF3 spec mentioned above. Currently, however, it is only designed to work with simple two-levelled features such as mRNA -> exon; or mRNA -> CDS; or similarity -> match_part.

 

A current workaround would be to re-load tracks as simple two-levelled features. I know this is not ideal, but at least that way you can be sure that the plugin is showing the borders correctly.

 

I hope this clears things up.

 

Best ,

 

Travis

 

From: Sofia Robb [mailto:[hidden email]]
Sent: Thursday, June 23, 2016 12:09 PM
To: [hidden email]
Subject: [Gmod-ajax] FeatureSequence Viewer Weridness

 

Most of the time I can get the viewer to display only the CDS sequence just fine, but occasionally I find that it does not. But it does highlight appropriately.

 

This might be because of the overlapping subfeatures, but I get errors about overlapping subfeatures for every transcript I have selected, most of which result in good sequence.

 

here is the error i get for the transcript for which I cannot get only the CDS sequence to display (but like I said, the appropriate CDS sequence can highlighted)

 

Warning: Overlap between features: exon_13 and CDS_14

Overlapping subfeatures will cause problems in viewing their boundaries.

This may also cause the Feature Sequence Viewer to respond slowly. 

 

 

to view only the CDS, I "Hide" all the subfeatures, then "Show" the CDSs. As you can see more than just the CDS (highlighted) is being dsiplayed

 

Inline image 1

 

What is interesting, is that when I hide all the subfeatures, there is still sequence displayed. I also noticed that there is no "other" subfeature listed.

 

Inline image 2

 

 

Thanks,

Sofia


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present their vision of the future. This family event has something for
everyone, including kids. Get more information and register today.
http://sdm.link/attshape
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