How exactly do I use BWA with paired-end reads?

[prs321]

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.

[chadn737]

1) Read the manual

2) Use them as a pair, ending up with 21 SAM files. Paired-end data is meant to be used as a pair.

[prs321]

Thank you, what would be the next step after creating 21 sam files? Are each of these 21 sam files basically the alignment of each pair to the index (.fasta file)?

[chadn737]

How am I supposed to know that? What are you trying to do?

As I pointed out in the other thread. You need to get a clear idea of what the end goal of the project is and then do some of your own research first, looking at papers and just googling around.