Why Do We Align Each Pair Set Separately In An Illumina Paired End Sequencing Study?
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12.5 years ago
Biomed 5.0k

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 • 2.7k views
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Entering edit mode
12.5 years ago
Swbarnes2 ★ 1.6k

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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