RNA-Seq is well known for calculating transcript expression. But, researches also do variant calling on RNA-seq data. In such case all mutations can't be identified due to alternative splicing. Also, there are notable difference in variants predicted from RNA-seq when compared with exome sequencing. In the case of exome sequencing all kinds of mutations can be identified which are in the coding region. My question : Can I perform Exome Sequencing for identifying transcript expression?
Hi,
"measuring the expression" in fact means measuring the amount of RNA. If you perform exome sequencing which is DNA-based, you simply do not obtain any information about RNA, therefore you cannot make any statements about expression.
Best wishes,
Michaela
Hi
well, exome sequencing will only be done on DNA and you'll understand and there will be no way to compute expression. all enrichment technologies you'll choose when replacing DNA by RNA will fail, less or more.
fred
Hi,
"measuring the expression" in fact means measuring the amount of RNA. If you perform exome sequencing which is DNA-based, you simply do not obtain any information about RNA, therefore you cannot make any statements about expression.
Best wishes,
Michaela
While genomic variants transcribe (if in transcribable regions) into the RNA, and thus you may detect it in RNA-Seq experiment, there is no way that analyzing gDNA will give you any information regarding the amount of expressed RNA...
Thank You... Jernej Kovac, Michaela Kotrová, Frederic Lepretre
My aim is to identify mutated genes in the coding region and genes that are expressed in that sample. To achieve my target what kind of sequencing method should I follow?
Hi
you can expect to detect variants in RNAseq studies but the best way in your purpose is to do both, exome sequencing based on DNA and RNAseq analysis on the same samples, more expensive but more reliable.
fred
Hi Frederic,
Are there any disadvantages on performing variant calling on RNA-Seq?
OR
What are the advantages of Exome seq over RNA-Seq in variant calling?
hi Snijesh,
The "only" disadvantage will be that on RNAseq only expressed genes will be sequenced and depending on the overall coverage lot of genes will be forgotten, compared with exome sequencing where all exons for all genes (some exceptions) are covered (allmost 80% of the exome will be covered, due to bias of GC%... that mess the enrichment of all genes). I said only but it's a big disadvantage of course, but you can therefore focus on your expressed genes of interest, a way to filter the analysis.
fred
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