I want to align reads in 2 different files using paired-end alignment with the help of bowtie. when I try to align it with bowtie1 it fails and a little portion of it just align to the reference genome. I aligned each file separately as a single read and when checked 2 SAM output files I saw that the flag values for entries in first file and second file are 0 for some entries and 16 for others,which I think means that some reads for each file were on the + starnd and others on - strand also when flag value for entry number N is 0 for first file it's corresponding flag value for N'th entry in second file is 16 . I want to know what should to do if i want to align it bowtie1? Is it true if I reverse all entries in first file and make all reads of first file on the same strand and do the same thing for second strand and then align it?
other question is that bowtie2 can map these two files, how can I be sure that mapping is true?