Forum: Possible Analysis from Data - RNA-Seq and Whole Genome Sequence
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gravatar for thekid2018
4.9 years ago by
thekid20180
United States
thekid20180 wrote:

Hello Everyone,

   I am new to the land of NGS and I have been tasked with some work that involves sequencing of paired : normal vs tumor samples by RNA-Seq  and Whole Genome Sequencing.

   As much as I have read and understood about NGS, I believe these are the data types that will be available for me to work with, could someone tell me if I missed something:

RNA-Seq----> SNPs, RNA edits, Isoforms, ncRNA, Gene Expression, Novel/Fusion transcripts.

Whole Genome Seq (WGS)----> SNPs, Indels, CNVs, LOH, SVs

Also could someone tell me how to determine the mutation rates for each sample either from RNA-Seq or WGS  (normal vs tumor)??

 

Thank you,

Vip

  

 

  

rna-seq next-gen forum genome • 2.6k views
ADD COMMENTlink written 4.9 years ago by thekid20180

It seems to me that, strictly speaking, RNA-Seq alone couldn't distinguish sequence variants (especially somatic mutations) and RNA edits without complementary WGS data. As for the mutation rates, RNA-Seq could miss some mutations or provide wrong frequency estimates due to gene expression bias.

ADD REPLYlink modified 4.9 years ago • written 4.9 years ago by mikhail.shugay3.3k
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