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?
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.
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