Amos With Paired End Data

Question

[Lee Katz]

Hi all, how do I take advantage of paired end data with AMOS? I have a 2x100bp fastq file that I would like to use AMOScmp-shortreads with. I see that when I google for it, there might be a .mates file or a switch to use with toAmos or toAmos_new but I am not sure of the exact command. Thank you.