Originally posted by NextGenSeq
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OK, so that is not "gene prediction" as mentioned in the first post -if i get it right. If you want to automatically annotated gene structures on a genomic sequence, then look for something like G-Morse or Cufflink, or a traditional gene finder. -
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i bet on deletion insertion polymorphism.Comment
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Originally posted by NextGenSeq View Post
Hi guys,
I'm having the same problem using CLC ... and I couldn't find any viable solution...About this pdf... is it from Clc? Because not even using their example data from the 'Annotation Plug-in' we could make it work.Comment
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If you're looking to do basic analysis have a look at some open solutions e.g. DIYA. It's quite simple to run a set of programs in serial. The hard part with annotation is manual curation and Artemis is a good tried and tested option. Geneious has some good offerings and it is prettier.Comment
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We are trying to know where the coding exons and SNPs are, to see if our snps are on coding regions.
We tried to import one annotated reference genome and only the annotation file (GFF) but none of this approaches worked.Comment
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Note CLC Bio will import the reference genome file from GenBank with the annotations. The files get very large if you include all the annotations. However, for small genomes it can handle all the annotations.Comment
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Using Arthemis we can import the annotations, but using CLC and the same GFF annotation file we can't.
The problem using Artemis is that we are having problem extracting the snps annotations in CLC... so in one program we have the exon annotations and in CLC we have our snps annotations.Comment
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