Unexpected deletions inside of an exon for cDNA sequences

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Unexpected deletions inside of an exon for cDNA sequences

Loraine Guéguen
Hi,

We are facing a problematic issue :

A frameshift is created inside an exon after drag and drop of a gene
(see the first screenshot), which introduces a stop codon.
Doing multiple alignment on the sequences, it appears that there are
deletions in the cDNA sequence.

In the second screenshot, you can see the alignments located on the
problematic exon for:
- the reference sequence
- the evidence sequence (EVM)
- the user-created gene (genomic)
- the user-created gene (cDNA)
- the user-created single exon (genomic)
- the user-created single exon (cDNA)

You can see that whereas the genomic sequences are correct, the cDNA
sequences have 2 deletions. That is strange !
Do you have any clue about what is happening ?


We have Apollo 2.0.4


Thanks,

Loraine Guéguen



--
Loraine Guéguen

Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)
Service Informatique et Bioinformatique
Station Biologique de Roscoff
FR 2424 CNRS UPMC
Place Georges Teissier
CS 90074
29688 Roscoff cedex
tel: ++33 (0)2 98 29 56 46 (interne : 415)
http://abims.sb-roscoff.fr/
http://www.sb-roscoff.fr/





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frameshift_apollo.png (31K) Download Attachment
seq_alignment.png (23K) Download Attachment
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Re: Unexpected deletions inside of an exon for cDNA sequences

Deepak Unni
Hi Loraine,

Would it be possible to share the reference genome and the GFF3 for the Evidence Modeler prediction track? 
If its difficult to share the entire GFF3 then just the feature in question would suffice. It would help in local testing and debugging.

If you would like to send it directly then here is my email: [hidden email]

Thanks,

Deepak

On Fri, May 26, 2017 at 10:31 AM, Loraine Guéguen <[hidden email]> wrote:
Hi,

We are facing a problematic issue :

A frameshift is created inside an exon after drag and drop of a gene (see the first screenshot), which introduces a stop codon.
Doing multiple alignment on the sequences, it appears that there are deletions in the cDNA sequence.

In the second screenshot, you can see the alignments located on the problematic exon for:
- the reference sequence
- the evidence sequence (EVM)
- the user-created gene (genomic)
- the user-created gene (cDNA)
- the user-created single exon (genomic)
- the user-created single exon (cDNA)

You can see that whereas the genomic sequences are correct, the cDNA sequences have 2 deletions. That is strange !
Do you have any clue about what is happening ?


We have Apollo 2.0.4


Thanks,

Loraine Guéguen



--
Loraine Guéguen

Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)
Service Informatique et Bioinformatique
Station Biologique de Roscoff
FR 2424 CNRS UPMC
Place Georges Teissier
CS 90074
29688 Roscoff cedex
tel: <a href="tel:%2B%2B33%20%280%292%2098%2029%2056%2046" value="+33298295646" target="_blank">++33 (0)2 98 29 56 46 (interne : 415)
http://abims.sb-roscoff.fr/
http://www.sb-roscoff.fr/





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.





--
Research Analyst
S104A Animal Science Research Center,
University of Missouri, Columbia




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