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

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

next-gen sequencing

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updated 14.5 years ago by Swbarnes2

• written 14.5 years ago by Biomed

1 answer

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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written 14.5 years ago by Swbarnes2

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