I'm mapping two samples independently (PE reads) using bwa-mem:
bwa mem -t 3 -M ref.fasta sample1_R1.fastq sample1_R2.fastq > sample1.sam # (2121026 mapped reads) bwa mem -t 3 -M ref.fasta sample2_R1.fastq sample2_R2.fastq > sample2.sam #(2485112 mapped reads)
But when I pool reads from two samples together and map them the number of mapped reads is higher: 5315859 reads vs 4606138. Why is this happening? Don't the reads map independently?