UGENE Forum - RT-PCR Primer Design failed to search for exon annotations

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UGENE Forum › General Category › Bugs and Issues › RT-PCR Primer Design failed to search for exon annotations

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RT-PCR Primer Design failed to search for exon annotations (Read 5658 times)

Nov 14^th, 2017 at 10:03pm

fbalao Offline
YaBB Newbies

Posts: 2

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 | 318 )

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Reply #1 - Nov 15^th, 2017 at 10:01am

Olga Golosova Offline
YaBB Administrator

Posts: 338

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)?

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Reply #2 - Nov 15^th, 2017 at 3:25pm

fbalao Offline
YaBB Newbies

Posts: 2

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

scaffold1126.fa (89 KB | 342 )

scaffold1126_annotations.gb (0 KB | 327 )

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Reply #3 - Nov 16^th, 2017 at 6:46pm

Olga Golosova Offline
YaBB Administrator

Posts: 338

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!

scaffold1126_with_added_features.gb (113 KB | 327 )

export_seq_with_ann_1.png (68 KB | 307 )

export_seq_with_ann_2.png (45 KB | 315 )

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