Annotation of NGS data with CLC Bio

[Anelda]

I have come across several very good tools designed specifically for annotation, but I've been told that CLC can give me the same annotation. Unfortunately no-one can tell me how to get it from CLC. I was hoping someone in the community has had some experience. Sorry, I realize this is moving a bit away from NGS.

Any help would be much appreciated

[KevinLam]

I would actually use artemis instead

http://www.sanger.ac.uk/resources/software/artemis/

I believe CLCbio has the ability to do the same. But I got lost in the menus.
artemis was written to serve this purpose only and it handles embl format which might be useful for submission.

but correct me if I am wrong, you are not really trying to annotate NGS data but contigs derived from NGS data.

[husamia]

can you give some example of what you mean by annotate?

[Anelda]

I think this might be it: http://www.clcbio.com/index.php?id=1343

Hi, thanks for your help. This is unfortunately to upload a gff file. That means you have already annotated the genome and have created a gff file and just want to upload your annotations. What I am looking for is how to actually create such a file using CLC - if this can be done.

Thanks again.

[kopi-o]

I think this might be it: http://www.clcbio.com/index.php?id=1343

[Anelda]

Can someone please send the pdf or refer me to the link where I can find it?

[NextGenSeq]

Yes, there is a pdf posted previously on how to do this. Note for large mammalian genomes the files become very large with each annotation added. For human I usually just annotate the exons and SNPs.

[Anelda]

Hi there,

Has anyone used CLC Bio (or can it be used) to annotate complete genomes or large contigs obtained from either de novo assembly or mapping to a reference genome? I'm talking about gene prediction, TFBS finding, GO annotation etc.

Thanks!