Question: SNPEFF for de novo transcriptome annotation
0
gravatar for Arsalan
3 months ago by
Arsalan10
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 3 months ago by moushengxu270 • written 3 months ago by Arsalan10
3
gravatar for prasundutta87
3 months ago by
prasundutta87150
prasundutta87150 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 3 months ago by prasundutta87150
3
gravatar for moushengxu
3 months ago by
moushengxu270
moushengxu270 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 3 months ago by moushengxu270

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

ADD REPLYlink written 3 months ago by WouterDeCoster23k
1

Well said! :)

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

ADD REPLYlink written 3 months ago by moushengxu270
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 935 users visited in the last hour