Question

Export error WITH AGP?

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6.8 years ago

PK ▴ 130

Dear all, I am doing de novo assembly (aspergillus flavus) in clc genomics workbench when i export assembled file in fasta format i am getting error.

Export AGP

Export error: The scaffold region did not cover a region with N's (Annotation name: Scaffold Type: Scaffold: Region: 12036..12037 in CI21_(paired)_contig_2

Please explain me and how to solve this

software error genome next-gen alignment • 1.4k views

ADD COMMENT • link updated 4.6 years ago by Jonathanjacobs ▴ 280 • written 6.8 years ago by PK ▴ 130

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Since you are using commercial software the company should also offer you support on these issues.

ADD REPLY • link 6.8 years ago by WouterDeCoster 47k

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Okay, but i am using trail version

ADD REPLY • link 6.8 years ago by PK ▴ 130

score 0 · Answer 1 · 2019-10-10

I know this is 2+ years old - but

1/ this may have been a bug at the time if you were trying to directly export a de novo assembly to FASTA. The work around was to first call consensus contigs from the assembly graph, and then export that.

2/ in the latest version (GxWB12 as of this writing) you can dump FASTA directly from assembly results without issue.