Question

SNPEFF for de novo transcriptome annotation

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7.3 years ago

Phismil ▴ 20

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 • 2.2k views

ADD COMMENT • link updated 7.3 years ago by moxu ▴ 510 • written 7.3 years ago by Phismil ▴ 20

score 3 · Answer 1 · 2017-07-28

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

score 3 · Answer 2 · 2017-07-28

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7.3 years ago

moxu ▴ 510

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

ADD COMMENT • link 7.3 years ago by moxu ▴ 510

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

ADD REPLY • link 7.3 years ago by WouterDeCoster 47k

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Well said! :)

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

ADD REPLY • link 7.3 years ago by moxu ▴ 510