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Annotation Pipeline For Snpeff

For genomes on which I work on are only the anchestors avaible. Therefore I used GlimmerHmm which has trained dataset in (GlimmerHMM/trained_dir) and it predicted genes in a GFF3 file format.

Unfortunately, snpEff predicted less effects than in snpEff's paper described and also the gene names were missing. Therefore, I am not sure whether I have to use another tool after GlimmerHMM in order to provide more information about the genes.

Is there any good annotation pipeline avaible?

Thank you in advance.

annotation pipeline gene prediction
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updated by Michael Dondrup Michael Dondrup • written by ric • ric

Please provide more details and revise your question. Which organism, which genome assembly? What do you mean by "only the anchestors avaible"? Why do you assume your approach is going to work properly and is appropriate at all using Glimmer? Why is it a problem that "snpEff predicted less effects than in snpEff's paper" on a rough gene prediction? Is it surprising at all that a de novo gene prediction has no gene names???

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written by Michael Dondrup Michael Dondrup

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