can add_transcripts_from_gff3_to_annotations.pl import substitution and stop_codon_read_through features?

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can add_transcripts_from_gff3_to_annotations.pl import substitution and stop_codon_read_through features?

Monica Poelchau
Hi everyone,

We've been using add_transcripts_from_gff3_to_annotations.pl to move manual annotations from Apollo1 to Apollo2 (and aren't using migrate_annotations1to2.groovy for direct transfer for various reasons). So far so good, but two feature types have me stumped: substitutions and stop_codon_read_throughs. Any thoughts on how to handle these would be appreciated!

Substitutions: I've sort of been able to import substitutions by specifying '-g substitution -G substitution' in the loading script. However, what format does the nucleotide substitution itself need to have for Apollo2 to recognize it? I've tried adding a seq attribute (e.g. seq=A where A is the nucleotide that will substitute the original) to column 9 of the gff. The substitution loads, but the value of the substitution is 'undefined' after import.

stop_codon_read_through: I'm not sure where to start here. These features are modeled as child features of the CDS in Apollo1 - but should I make them child features of the mRNA, instead, and use '-d stop_codon_read_through -D stop_codon_read_through' or '-e stop_codon_read_through -E stop_codon_read_through'?

Thanks!

Monica




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Re: can add_transcripts_from_gff3_to_annotations.pl import substitution and stop_codon_read_through features?

nathandunn
Monica,

The original idea (back to Apollo 1) was that add_transcripts_from_gff3_to_annotations.pl would be taking in annotations against a published reference sequence (i.e., alterations were already integrated).  

However, we can add support for both of these to support the case of folks migrating while still in the middle of annotation.  I created an issue to track the enhancement here:

https://github.com/GMOD/Apollo/issues/1514

Nathan


> On Mar 3, 2017, at 8:30 AM, Monica Poelchau <[hidden email]> wrote:
>
> Hi everyone,
>
> We've been using add_transcripts_from_gff3_to_annotations.pl to move manual annotations from Apollo1 to Apollo2 (and aren't using migrate_annotations1to2.groovy for direct transfer for various reasons). So far so good, but two feature types have me stumped: substitutions and stop_codon_read_throughs. Any thoughts on how to handle these would be appreciated!
>
> Substitutions: I've sort of been able to import substitutions by specifying '-g substitution -G substitution' in the loading script. However, what format does the nucleotide substitution itself need to have for Apollo2 to recognize it? I've tried adding a seq attribute (e.g. seq=A where A is the nucleotide that will substitute the original) to column 9 of the gff. The substitution loads, but the value of the substitution is 'undefined' after import.
>

> stop_codon_read_through: I'm not sure where to start here. These features are modeled as child features of the CDS in Apollo1 - but should I make them child features of the mRNA, instead, and use '-d stop_codon_read_through -D stop_codon_read_through' or '-e stop_codon_read_through -E stop_codon_read_through’?
>
> Thanks!
>
> Monica
>
>
>
> This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
> If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.
>




This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
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