Methodology Flashcards
What are the other pipelines? How are they done? How does it par with the DugesiaAMR pipeline?
How are MGEs identified in other studies? How did you do it?
Why is mapping against multiple references at the same time preferred to mapping against multiple different references 1 at a time?
Mapping scores and alignment scores are both related to how confident the mapping program is that an individual read is mapped to the correct location in the genome, and how well that that read aligns at that location.
If you map against both references at the same time, the mapper will associate each read uniquely to either the plasmid region or the chromosome without having any mismatches.
If you map against the references separately, both will result in 50% of the reads aligned to this region as having a high quality mapping score, and a slightly diminished alignment score for both runs.
