I have reads containing E. coli, K. pneumoniae and GAPDH spike-in. I would like to align these reads to the 3 genomes and then discard reads that map to more than one of the references.
So far, I have concatenated all 3 fasta files into 1 composite genome. I have then used
bwa mem -c 1 <composite_genome.fasta> <Sample_x_R1> <Sample_x_R2>.
Can I check if this would be the correct way to do this or have I gone wrong somewhere?