Question: Normalized non-synonymous variant count
0
gravatar for qwzhang0601
3.8 years ago by
qwzhang060160
United States
qwzhang060160 wrote:

I am analyzing 1000 genome data and get the annotation of SNP by ANNOVAR. Now I want to normalize the synonymous and non-synonymous variant count in a group of genes according to the length of genes. Because each gene may have different isoforms, I choose the longest transcripts and use their lengths.   I wonder whether it is right? should I use the length of CDS (since there are UTR in transcript, which are not translated)? Thanks

 

 

snp gene • 1.1k views
ADD COMMENTlink modified 3.8 years ago • written 3.8 years ago by qwzhang060160

Well you're probably not going to have any non-synonymous mutations in an untranslated region. So If you want the numbers to skew....


 

ADD REPLYlink written 3.8 years ago by karl.stamm3.4k
0
gravatar for qwzhang0601
3.8 years ago by
qwzhang060160
United States
qwzhang060160 wrote:

Thanks. Do you prefer to use the length of longest CDS instead of the longest transcript?

ADD COMMENTlink written 3.8 years ago by qwzhang060160
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: 1188 users visited in the last hour