BWA, fastq reads mapped to multi ref fasta. ALL vs ALL

Question

[erneheay]

I have a fasta with two or more references. I want to map ALL my reads (fq) to both references.

What happens now, bwa chooses which is the best reference for each paired read, and it's discarded for the other reference.

I want exactly the same behavior than mapping separately using two different fasta files (with one ref each).

Is it possible?

Cheers

Answer 1

[colindaven]

Just map to each fasta ref completely separately , i.e. split the fasta before alignment ? BTW, alignment is NOT assembly, see your tags.