Question: Identifying Non Synonymous mutations in bacterial genomes
0
gravatar for mmart12
4.0 years ago by
mmart1220
European Union
mmart1220 wrote:

Hello, I would like to discriminate non-synonymous mutations from synonymous mutations in bacterial genome sequences. In particular, I have got a list of mutations between a query and the reference genome obtained through the software breseq. I have used snpeff but I got problem because the software listed some mutations as "upstream gene variant" where in fact the mutation occurred in a gene. So i guess I can't really trust snpeff.
Do you know other software or script I can use?
And also, once I got the non synonymous mutations do you know how I can assess if they are deleterious or not?

Thank you very much

sequence snp next-gen R genome • 1.2k views
ADD COMMENTlink written 4.0 years ago by mmart1220

I too work on bacterial WGS. Did you try silencing that option in snpEFF?? I have used freebayes to call my variants and have never tried breseq. Sometimes even if the gff3 file does  have a proper formatting it might spring up many messages on the screen. Try using Polyphen,snpgo,predprotein,SIFT. I know still more but not able to recall.....

ADD REPLYlink written 4.0 years ago by alok.helix80
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: 1153 users visited in the last hour