RNA-Seq Quantification

Question 0

What is TopHat?

Answer 0

A software that aligns cDNA fragments to the genome, and is able to produce spliced alignments.

Question 1

What is cufflinks?

Answer 1

software that quantifies transcript abundance

Uses dilworths proof to produce a minimal set of paths that cover all the fragments in an overlap graph by finding the largest set of reads with the property that no two could have org instead from same isoform

Question 2

Dilworths theorem

Answer 2

The number of mutually incompatible reads is the same as the minimum number if transcripts needed to “explain” all the fragments

Question 3

What is eXpress?

Answer 3

Software package that assigns ambiguously mapped sequence in real time using streaming algorithm

Question 4

What is Transcript quantification ?

Answer 4

Estimation of relative abundance, at both the gene and isoform levels

1) RNA seq
2) mapping reads to reference genome
3) estimate abundance based on read mapping p

Question 5

RSEM

Answer 5

RNA-Seq by Expectation maximization

• does not depend on reference genome
• requires reference transcript sequences