QUIZ#2

Class 5 quiz

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Flag question: Question 1

Question 1 1 pts

What is meant by an instrument “run” as this relates to sequencing?

Group of answer choices

a. The process of going from sample to sequence one time

b. The amount of time it takes to go from sample to sequence

c. The massively parallel application of sequencing technology.

d. The amount of material it takes to go from sample to sequence

 

Flag question: Question 2

Question 2 1 pts

For 1000 reads of 100 bases each mapping to a 10,000 base genome, what is the approximate fold coverage you expect?

Group of answer choices

a. 20

b. 50

c. 12

d. 10

 

Flag question: Question 3

Question 3 1 pts

How does mate pair information aid assembly?

Group of answer choices

a. Redundancy helps confirm genotypes

b. Increased coverage increases accuracy

c. Longer effective length can span gaps

d. All of the above

 

Flag question: Question 4

Question 4 1 pts

How can mate pairs “rescue” reads corresponding to non-unique genome regions?

Group of answer choices

a. Two ends of a mate pair act together to increase read length and allow rescue.

b. An otherwise ambiguous read maps uniquely when constrained by its mate

c. If two reads partially overlap, the ambiguous one can be rescued.

d. None of the above

 

Flag question: Question 5

Question 5 1 pts

For a sample with a homozygous deletion, what pattern is seen in mate pair data when mapped to a reference? It may help to draw a picture of your DNA mapped to the (frame of) reference sequence.

Group of answer choices

a. This will depend primarily on read length and uniqueness.

b. Mate pair reads may be partially or completely missing.

c. Mate pair reads will map the reference further apart than expected.

d. Mate pair reads will map the reference closer together than expected.

 

Flag question: Question 6

Question 6 1 pts

For an insertion, what pattern is seen in mate pair data? It may help to draw a picture of your DNA mapped to the (frame of) reference sequence.

Group of answer choices

a. This will depend primarily on read length and uniqueness.

b. Some mate pair reads will map the reference further than expected while others will be closer than expected.

c. Mate pair reads will map the reference further apart than expected.

d. Mate pair reads will map the reference closer together than expected and may have unmapped reads at one end.

 

Flag question: Question 7

Question 7 1 pts

What is the (general class of) algorithm used to determine read overlap?

Group of answer choices

a. Heuristic search followed by matching

b. Graph node matching

c. Sequence score matching

d. String alignment

 

Flag question: Question 8

Question 8 1 pts

If you use M reads, what is the minimum number of pair-wise overlaps that must be computed for building an assembly? For this, an "overlap" means alignment and may be considered a single operation. If your stuck, try for a few small values of M: M=3, 4,..)

Group of answer choices

a. Approximately 2 to M'th power.

b. M * ( M - 1) / 2

c. Not enough information

d. M * M

 

Flag question: Question 9

Question 9 1 pts

In the context of modern (de Bruijn) graph based assembly algorithms, what is considered a "node"?

Group of answer choices

A. A k-mer

b. A read

c. Mate pair reads

d. Overlap between reads

 

Flag question: Question 10

Question 10 1 pts

In the context of modern (de Bruijn) graph based assembly algorithms, what is considered an "edge"?

Group of answer choices

a. A k-mer

b. A read

c. Mate pair reads

d. Overlap between k-mers

 

Flag question: Question 11

Question 11 3 pts

What is a heuristic? Can you think of a heuristic to reduce the number of full-blown sequence alignments needed for assembly using M reads?

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