What is the difference between Exome sequencing versus RNA sequencing ? What type of de novo assemblers should be use for exome sequencing reads and what de novo assemblers for RNA sequencing reads?
Dear Abdul,
Generally we do exome sequcing to know the presence of active gene in genome but in case of transcriptome sequencing we target only transcript to know their expression level.
After whole transcriptome Sequencing things has been little bit complex to clarify that its same or not. Transcriptome sequencing can explain the level of expression. In few cases Bioinformaticians and typical Molecular Biologist differentiate between Exom and Transcriptome Sequencing that Exome is basically DNA Based sequencing and transcriptome is RNA based sequencing, which is not so well explanation.
I hope this much of information will help you to clear your doubt.
Best Regards
Piyush
Dear
1-In definition Exome sequencing, is a technique for sequencing all of the expressed genes in a genome (known as the exome).
Exome sequencing offers a look into the genome that large-scale studies of common variation, such as the genome-wide association study (GWAS), cannot provide. GWAS can only identify variation in DNA that is common in the population, in at least one percent of people.
-Gilbert W (February 1978). "Why genes in pieces?". Nature 271 (5645): 501.
2-RNA-Seq (RNA sequencing), also called whole transcriptome shotgun sequencing (WTSS), uses next-generation sequencing (NGS) to reveal the presence and quantity of RNA in a biological sample at a given moment in time.
-Ryan D. Morin; Matthew Bainbridge; Anthony Fejes; Martin Hirst; Martin Krzywinski; Trevor J. Pugh; Helen McDonald; Richard Varhol; Steven J.M. Jones & Marco A. Marra. (2008). "Profiling the HeLa S3 transcriptome using randomly primed cDNA and massively parallel short-read sequencing". BioTechniques. 45 (1): 81–94. .
-Chu Y, Corey DR (August 2012). "RNA sequencing: platform selection, experimental design, and data interpretation". Nucleic Acid Ther. 22 (4): 271–4.
Best regards
Marius
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2949280/
https://www.ncbi.nlm.nih.gov/pubmed/622185
Dear Adbul,
For exome sequencing you map your reads against your reference genome and do your downstream analysis. This is not a de novo assembly.
For RNA-seq you can also do a de novo assembly with e.g. Trinity (one of the most usage tool) or a referece-guided assembly with e.g. BWA, STAR and others. This choice depends on your goals.
Lets us know if you want more information about each approach.
Best,
Michele
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4528311/
See: A Beginner’s Glance at RNA sequencing vs. Exome sequencing
http://www.rna-seqblog.com/a-beginners-glance-at-rna-sequencing-vs-exome-sequencing/
Exome sequencing looks at the DNA contained in exonic regions of the genome while RNA-Seq looks at RNA transcribed from DNA, much of which, but not all, derives from the exonic regions.
While both RNA-Seq and exome sequencing are related to the protein-coding portion of the genome, these two applications approach it from different starting points. The exome is the protein- coding portion of the genome (~2% of mammalian DNA), comprised of exons. Sequencing the exome involves a targeted approach to sequence just that portion of the DNA (generally by fishing out that portion of the genome with pre-designed oligos). The end result is DNA sequence that is highly enriched for DNA from exons (but with varying levels of off-target DNA). It's generally used to look for DNA differences between samples (e.g., patients when used in a clinical setting). It is often chosen as a substitute for whole genome due to its lower cost, lower data storage and analysis requirements, and when ultra deep sequencing is desired (e.g., looking for rare mutations).
RNA-Seq is a method for looking at the portion of DNA that has been transcribed into RNA at a given time. While RNA-Seq is often used to look just at the complement of RNA that is derived from exons (e.g., the exome), there are RNAs which fall outside of this region (e.g., introns, intergenic regions, small RNAs, etc). Another key difference is that the RNA component is not static - the levels of RNA for the various genes will vary over time, from individual to individual, and from tissue to tissue in the same individual (while the exome will remain static, barring any mutations)
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