i want to map my own reads (illumina hiseq) to reference using "bwa mem". i have 2 lane of paired end data (read1.fastq, read2.fastq, read11.fastq and read22.fastq). in bwa tutorial, command for map to reference of paired end reads is "bwa mem ref.fa read1.fq read2.fq > aln-pe.sam". now i have 4 read files for mapping to reference, what is command for my reads?
"bwa mem ref.fa read1.fq read2.fq read11.fq read22.fq> aln-pe.sam" is true?