I am currently aligning some sequences that contain numerous chimeric reads using bwa (paired-ends). Usually, first third of the R1 is on Chr1 and the rest on Chr18, the R2 is fully mapped to Chr18.
I was wondering how bwa was aligning those reads. If we look at the sam file produced after alignment, what will be the RNAME of the read R1 (chr1 or chr18)? And how is it decided?
Thanks in advance!