I'm trying to align a 3.5K-insert mate-pair library using MAQ 0.7.0. From the man page (http://maq.sourceforge.net/maq-manpage.shtml), it is not quite clear to me how exactly MAQ handles the outward orientation of such reads, and how it distinguished paired-end input from mate-pair input. Do I have to pass the files in reverse order, i.e. R.fq F.fq? Do I have to reverse the sequences within the files? Both? Nothing?
Any help is greatly appreciated :-)