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https://forum.ugene.net/forum/YaBB.pl General Category >> Bugs and Issues >> RT-PCR Primer Design failed to search for exon annotations https://forum.ugene.net/forum/YaBB.pl?num=1510671827 Message started by fbalao on Nov 14^th, 2017 at 10:03pm

Title: RT-PCR Primer Design failed to search for exon annotations
Post by fbalao on Nov 14^th, 2017 at 10:03pm

Hi,
I'm having a error using the RT-PCR Primer Design. It seems UGENE can't detect my exon annotations. Any idea?

Task report [Search primers to annotations]
Error: Subtask {FindExonRegionsTask} is failed: Failed to search for exon annotations. The sequence scaffold1126 doesn't have any related annotations.

Thanks in advance

ugeneissue.jpg (166 KB | 320 )

Title: Re: RT-PCR Primer Design failed to search for exon annotations
Post by Olga Golosova on Nov 15^th, 2017 at 10:01am

Hi!
I'm not able to reproduce the issue using our sample data. Could you please send us the scaffold1126 sequence (e.g. by email)?

Title: Re: RT-PCR Primer Design failed to search for exon annotations
Post by fbalao on Nov 15^th, 2017 at 3:25pm

Yes sure. Here, the scaffold and the annotation file. I'm using UGENE V1.26.3 in Ubuntu 14.04.

https://forum.ugene.net/forum/YaBB.pl?action=downloadfile;file=scaffold1126.fa (89 KB | 344 )

https://forum.ugene.net/forum/YaBB.pl?action=downloadfile;file=scaffold1126_annotations.gb (0 KB | 330 )

Title: Re: RT-PCR Primer Design failed to search for exon annotations
Post by Olga Golosova on Nov 16^th, 2017 at 6:46pm

It appears, that UGENE incorrectly processes annotations in case they are stored in a separate document. So as a workaround, you need to export the sequence and the annotations into a single GenBank file. See the screenshots and the result file in the attachment.

Thanks for informing us about this problem!

https://forum.ugene.net/forum/YaBB.pl?action=downloadfile;file=scaffold1126_with_added_features.gb (113 KB | 330 )

export_seq_with_ann_1.png (68 KB | 311 )

export_seq_with_ann_2.png (45 KB | 319 )