NGS result with alteration: how to find whether the alteration will bring amino acid substitution?
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Entering edit mode
5.3 years ago

Hi there, I ask a favour to you.

I had NGS with 4 bacteria, to say S1, S2, R1, R2 with a reference F.

Each of the alteration results are based on the compare to F.

What Im going to do is,

1. comparing the alteration difference between S and R and

2. to check the alterations of R compared to S, changed the amino acid of the site; yes, to find the type of mutation whether it is a synonymous or non-synonymous​ mutation.

I've solved the question 1. by myself with simple functions of excel.

By the way, it is too large amount of data and complicated functions are needed to do with excel.

Im finding tools or any methods that can do

1. changing a genome sequence with listed alteration on excel or

2. one blackmagic-like tool that fit for my situation.

Thank you for your warm-hearted favour!

Open SNP NGS • 986 views
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Entering edit mode
5.3 years ago

You'll do yourself a favor by not using Excel for any of this.

For comparing variants you can use things like VCFtools. For annotating them you can have a look at snpEFF or "variant effect predictor", which is from Ensembl.