Question: detection of single nucleotide variations with RNA-seq
gravatar for mlemusfuentes
1 day ago by
mlemusfuentes10 wrote:

hello everyone,

I need know if someone has performance detection of single nucleotide variants (SNVs) using RNA-seq data. I know that the gold standard method is whole genome or exome sequencing (WGS or WES), but I need to implement a method less expensive for the determination of SNVs. I found a scientific paper written by Chepelev et al. 2009 which is entitled "Detection of single nucleotide variations in expressed exons of the human genome ( You know it protocol?, what are your appreciations of detection of SNVs using RNA-seq data?, what would be the weak points of this type of analysis?

I will appreciate any comments or advice

rna-seq snv • 47 views
ADD COMMENTlink written 1 day ago by mlemusfuentes10
gravatar for ATpoint
1 day ago by
ATpoint41k wrote:

This has been discussed many times before, please check previous threads:

Rna-Seq Data Variant Calling

Inferring genotype based on RNA sequences (RNA-seq variant calling)

What is the advantage of variant calling using RNA-seq technique?

RNA and DNA variant difference

and others via the search function.

I think the take-home message is that you can try and feed your RNA-seq data into a variant caller but you would need to more extensively confirm interesting variants with independent experiments. You are obviously limited to expressed exons.

ADD COMMENTlink modified 1 day ago • written 1 day ago by ATpoint41k

Moved to answer

ADD REPLYlink written 1 day ago by Kevin Blighe67k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2234 users visited in the last hour