I want to map the output of 4 separate illumina smrt cells against a pacbio reference genome using BWA. I've indexed the full genome.
I can try run the the equivalent of this line, but using additional reads:
bwa mem ref.fa read1.fq read2.fq > aln-pe.sam
However, if I try
bwa mem ref.fa read1.fq read2.fq read3.fq read4.fq > aln-pe.sam
include read3.fq or more nothing runs.. Instead I get the usage instructions for bwa.
Is there a way to map 4 illumina runs against the reference genome at once, or am I misunderstanding this process?
There are simply 4 runs to increase robustness.