Why Do We Align Each Pair Set Separately In An Illumina Paired End Sequencing Study?

Question

[Biomed]

Can you tell me why I need to align each set of reads (forward and reverse) seperately using BWA when I have paired end reads from Illumina? In other words, why do we need to have the reads in two files reads1.fastq and reads2.fastq? Thanks

Answer 1

[Swbarnes2]

bwa won't get that they are paired in the sampe stage unless you align them separately. Just look at the sampe command line. It expects separate files for each read.