Data preprocessing Flashcards
1
Q
Explaing fastQC
A
Shows quality, e.g. how much should be trimmed, removed (adaptors/primers) etc.
2
Q
What does k-mer correction do? What is it used for? What does it require?
A
A sliding window of k-mers - use it on all reads to count occurrence of each kmer.
Used to correct sequencing errors.
It requires sufficient coverage.
3
Q
Rule of thumb, what is the required coverage?
A
15X
4
Q
What is sequencing depth? How do you calculate it?
A
How many times does your data cover the genome (average).
Calculated from:
number of reads * read length / genome size
5
Q
What is breadth of coverage?
A
How much of reference is covered by data
6
Q
Why is assembly affected by the presence of adaptors but alignment is not (as much)?
A
Because alignment uses Smith-Waterman, a local alignment algorithm
