I have 42 fastq files (20 specimen and 1 ancestral). They are paired-end reads.
I am curious as to what I am supposed to do with BWA.
My questions:
1. How do I use BWA with paired-end reads?
2. If I use both files of a pair as an argument to align and map, do I do the same for every pair thus ending up with 21 SAM format files? Or do I just align and map each sequence so that I end up with 42 SAM format files?
Thanks.
I am curious as to what I am supposed to do with BWA.
My questions:
1. How do I use BWA with paired-end reads?
2. If I use both files of a pair as an argument to align and map, do I do the same for every pair thus ending up with 21 SAM format files? Or do I just align and map each sequence so that I end up with 42 SAM format files?
Thanks.
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