Yet another quality trimming question... I've got some Illumina paired-end DNAseq data from tumor and normal samples (100bp reads). I want to align the data using BWA mem, but I'm worried that some reads might be shorter than 70bp after quality trimming. Does anyone know how bwa mem handles such reads? Are they discarded?
For those who use bwa mem: do you do quality trimming at all?
For those who use bwa mem: do you do quality trimming at all?