Answer to Question #154931 in Bioinformatics for vaibhav

Question

(a) What is the output obtained from a RNA-seq experiment? Why do you have to remove rRNA and tRNA before performing RNA-seq?

(b) Why is mapping of RNA-seq reads more difficult than mapping re-sequencing reads or ChIP-seq reads? Explain.

(c) What is Phred quality score? Explain its use in RNA-seq experiment.

Answer 1

a) RNA-seq can tell us  which genes are turned on in a cell, what their level of expression is, and at what times they are activated or shut off.Removal of rRNA and tRNA before performing RNA-seq is necessary to achieve optimal coverage, good detection sensitivity and reliable results.

b) Mapping of  RNA-seq reads to the genome is more difficult than  mapping re-sequencing reads because many reads map across splice junctions

c)Phred quality score  is a measure of the quality of the identification of the nucleobases generated by automated DNA sequencing. The quality  of a given base call is measured as a Phred quality score and indicates the probability of the base being called correctly.