Question: How to know synonymous and non-synonymous SNPs from transcriptome sequencing
1
gravatar for smallfish
2.6 years ago by
smallfish10
smallfish10 wrote:

I obtained a SNP list (VCF format) from a sample's transcriptome (assembled by Trinity). ORFs were identified using TransDecoder. How I classify these SNPs? How to calculate ka/ks?

snp rna-seq • 2.1k views
ADD COMMENTlink modified 23 months ago by jfo0 • written 2.6 years ago by smallfish10
4
gravatar for Philipp Bayer
2.6 years ago by
Philipp Bayer6.8k
Australia/Perth/UWA
Philipp Bayer6.8k wrote:

You can annotate VCFs using SnpEFf, but you will first have to build the database: http://snpeff.sourceforge.net/SnpEff_manual.html#databases

This will (in the end) make a new VCF with non-synonymous SNPs and their severity (introduces STOP codons, changes AA, changes nothing etc.). SNPEff's report will also report the total number of Ka and Ks, if I remember correctly.

If you want to calculate Ka/Ks on a more detailed scale, use this script: https://github.com/MerrimanLab/selectionTools/blob/master/extrascripts/kaks.py which takes SNPEff's output and gives out a Ka/Ks table per gene

ADD COMMENTlink written 2.6 years ago by Philipp Bayer6.8k

Thanks very much. It's a good idea.

ADD REPLYlink written 2.6 years ago by smallfish10
0
gravatar for jfo
23 months ago by
jfo0
jfo0 wrote:

can we use SNPMeta for this? https://www.ncbi.nlm.nih.gov/pubmed/24237904

ADD COMMENTlink written 23 months ago by jfo0
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