Lecture 4 Flashcards
what is the number of reads generated for a specific base, or the number of reads covering a certain position in the targeted region?
read depth
what is the average number of reads considering all target regions that have been sequenced ?
coverage
what is the coverage indicated with?
a number and then an X
describe the sequence obtained after using Sanger sequencing:
a series of colors = series of nucleotides
what is the main problem with NGS data and sequencing?
there is a lot of variability among laboratories
what does the accuracy of NGS data depend on?
not only the quality of the sequencing but the the approach used for analysis
what are the three stages of NGS sequencing?
primary, secondary, and tertiary
what happens in the primary stage of NGS?
image capturing and processing
what happens in the secondary stage of NGS?
capture / sequence the read files
what happens in the tertiary stage of NGS?
variant interpretation
how is primary analysis performed?
on the sequencer itself
what is generated to measure the accuracy of the data generated in the primary stage?
phred score
what does the phred score indicate specifically?
the probability of a bae error being introduced into the variant coding
what occurs in secondary analysis?
variant calling
what is variant calling?
compares the reads obtained vs. the human reference genome and identifies all the variations present in the sample
