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SNPEFF for de novo transcriptome annotation

Dear Colleagues , I am just wondering if any one among you have ever tried SNPEFF for SNP annotation on species with out reference genome / transcriptome data available? I will appreciate any suggestions Many thanks in advance

snp assembly transcriptomics denovo
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updated by moxu moxu • written by Phismil • Phismil

2 answers

Snpeff annotates using the reference genome and its corresponding GTF/GFF file. If they are not available in ensemble, you will have to add and configure it manually. If you do not have a reference genome and its annotation, snpeff may not work at all. Check out: http://snpeff.sourceforge.net/SnpEff_manual.html#databases

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written by prasundutta87 prasundutta87

You need a reference genome. If you don't have a reference genome, maybe you can borrow one from a closest relative species.

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written by moxu moxu

Borrowing a reference genome is okay, but just don't forget to give it back when you are done!

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written by WouterDeCoster WouterDeCoster

Well said! :)

After returning the borrowed reference, make your own annotated genome the reference genome.

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written by moxu moxu

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