Question: SNPEFF for de novo transcriptome annotation
0
gravatar for Arsalan
8 weeks ago by
Arsalan10
United States
Arsalan10 wrote:

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

ADD COMMENTlink modified 8 weeks ago by moushengxu260 • written 8 weeks ago by Arsalan10
3
gravatar for prasundutta87
8 weeks ago by
prasundutta87110
prasundutta87110 wrote:

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

ADD COMMENTlink written 8 weeks ago by prasundutta87110
3
gravatar for moushengxu
8 weeks ago by
moushengxu260
moushengxu260 wrote:

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

ADD COMMENTlink written 8 weeks ago by moushengxu260

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

ADD REPLYlink written 8 weeks ago by WouterDeCoster21k
1

Well said! :)

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

ADD REPLYlink written 8 weeks ago by moushengxu260
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