Genome alignment
The reads are then mapped to the reference genome using the BWA-MEM algorithm (Langmead, Trapnell et al. 2009; Kim, Pertea et al. 2013). Only the reads mapped to the reference are used for further analysis.
The reads are then mapped to the reference genome using the BWA-MEM algorithm (Langmead, Trapnell et al. 2009; Kim, Pertea et al. 2013). Only the reads mapped to the reference are used for further analysis.