Variant Calling and Transcript expression from biological sample
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?
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
News: Cancer Genomics workshop
written by Physalia-courses
-
Can germline callers detect somatic variants? (RNAseq, cancer, no matched normal)
written by don •
-
Seeking Opinions on Pipeline for Detecting Somatic Variants and Rare Germline Mutations
written by George •
-
Which type of variant caller should I use in a WES normal cell line sample?
written by bompipi95 •
-
Blog: A Beginners Guide to DNA-seq: Bioinformatics Analysis
written by Novogene •
-
CNVkit calling strategies with matched-normal tumor
written by fbrundu
-
Forum: Types of sequencing and their precised use
written by Karma
-
RNA-Seq or Exome Seq for Clinical data analysis
written by Karma
-
Tutorial: Webinar on 'An integrated RNA and DNA approach to unravel genetic regulation in cancer' o…
written by Genomics
-
Tool: Varscan: Variant Detection In Massively Parallel Sequencing Data
written by Istvan Albert
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
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?