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Following are the aim of my study 1. Transcript/Gene expression 2. Variant calling (Mutations all kinds [germline, somatic, snp, indel, copy number etc]) For the aforesaid purpose, what kind of sequencing strategy should I follow? RNA-Seq or Whole Exome sequencing? Can you justify your answers?
Is this an assignment question? What have you tried?
If you feel it as an assignment question, I don't care. People with common sense can understand what I actually mean. In every blog there are some people like you with negative thoughts.
Well, that means that it is an assignment, am I right? What is negative about asking you what you have tried?
Please read this post first: How To Ask Good Questions On Technical And Scientific Forums
Well, it is not an assignment question. "What have you tried?", there is nothing negative in it. 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 1. Can I perform exome sequencing for identifying transcript expression?
@Snijesh no need for negative comments, Did you read my comment? did it answer your question? is there is any problem when people asking you to show what did you come so far to answer your own question so we can avoid repeating it?
For Transcript/Gene expression -> RNA-seq
Variant calling you can use either RNA-seq or whole genome (depends on what you want to achieve and also your budget)
please take look at this paper
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3791257/
Inconsistency and features of single nucleotide variants detected in whole exome sequencing versus transcriptome sequencing: A case study in lung cancer.
Exome versus transcriptome sequencing in identifying coding region variants
Thank You, I am focusing on expression and mutations in coding regions. In the case of RNA-Seq, we may loose some variants in the coding region when compared with exome sequencing. Can I perform Exome seq for identifying transcript expression?
To my knowledge No
10 Things Exome Sequencing Can t Do-but Why It s Still Powerful