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  • pedrotanno
    replied
    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.

    Leave a comment:


  • NextGenSeq
    replied
    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.

    Leave a comment:


  • pedrotanno
    replied
    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.

    Leave a comment:


  • zee
    replied
    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.

    Leave a comment:


  • pedrotanno
    replied
    Originally posted by NextGenSeq View Post
    CLC Bio is a bit buggy. You have to force import your reference genome as normal sequence data NOT next gen sequence data. Once you do that it is easy to annotate it using a GFF file. I tried attach the pdf describing it but this website gave an error message. If you private message me with your email address I can email it to you.

    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.

    Leave a comment:


  • steven
    replied
    i bet on deletion insertion polymorphism.

    Leave a comment:


  • bioinfosm
    replied
    sorry, but whats DIP?

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  • steven
    replied
    Originally posted by NextGenSeq View Post
    You have to annotate your reference genome to know where the coding exons and SNPs are. After the assembly and SNP/DIP detection the software tells you if the variations are coding or known SNPs. You have to know this for mutation discovery.
    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.

    Leave a comment:


  • NextGenSeq
    replied
    You have to annotate your reference genome to know where the coding exons and SNPs are. After the assembly and SNP/DIP detection the software tells you if the variations are coding or known SNPs. You have to know this for mutation discovery.

    Leave a comment:


  • steven
    replied
    I have the same question than husamia: what do you mean by "annotate"?
    Labeling a genomic region as a "contig/cluster/whatever of reads/ESTs/whatever" is one thing, performing automatic gene structure prediction is a totally different exercice (although both can produce a GFF file). I do not believe that CLC nor Geneious do the latter.

    Leave a comment:


  • johnny
    replied
    When you mark a base you can right-click on it and use the "Add Annotation".
    For extracting annotations you have to install a plugin called "Extract annotations"

    Welcome to QIAGEN Digital Insights LabCorp uses QCI and HGMD to improve identification and interpretation of genetic variants within inhereited diseases.Read...


    There you also find the "Annotate Sequence with GFF File" plugin.

    Leave a comment:


  • NextGenSeq
    replied
    CLC Bio is a bit buggy. You have to force import your reference genome as normal sequence data NOT next gen sequence data. Once you do that it is easy to annotate it using a GFF file. I tried attach the pdf describing it but this website gave an error message. If you private message me with your email address I can email it to you.

    Leave a comment:


  • alpapan
    replied
    alternatively

    Hey

    We've been using Geneious Pro rather successfully to accomplish this for small contigs (I guess it depends how much memory your computer has). It allows to annotate a sequence, export it as GFF. You can also import other GFFs as annotations only (i.e. if it is a GFF file without a FASTA section but you have a geneious document with the reference sequence).

    Geneious is also prettier than CLC bio and much much cheaper...

    cheers,
    a

    Leave a comment:


  • Anelda
    replied
    Originally posted by KevinLam View Post
    You did pay for the software so support is obligatory
    That's just the thing. Haven't bought it yet. Still trying to determine what percentage of our work could be done on it. Have the trial version. The vendor has been helpful, but not really answering my question so far. That's why I've gone to the community in the meanwhile. Will poke the vendor again today.

    Leave a comment:


  • KevinLam
    replied
    Oh no worries, just wanted to clarify the problem in case I am misunderstanding the question.
    I would think that commercial providers would be able to help your question better?
    You might get an answer here but I would think getting info from the source would be much more directed and helpful?
    You did pay for the software so support is obligatory

    Leave a comment:

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