The first program of the STACKS pipeline, is "ustacks". According to https://catchenlab.life.illinois.edu/stacks/manual/#phand
"...# Build loci de novo in each sample for the single-end reads only. If paired-end reads are available, they will be integrated in a later stage (tsv2bam stage)."
and "...tsv2bam will use the single-end read IDs from the assembled loci to find the corresponding paried-end reads in the sample_XXXX.2.fq.gz files."
I have 2 files from each sample, one forward and one reverse read. Does this mean that I only apply the ustacks program to the forward reads? But what is confusing me here is that the reverse ends are "independent" reads from the forward reads, i.e., they are not overlapping. So what does this second statement mean? How is it going to find the "corresponding" paired-end read, if they are not overlapping (there's a gap between the forward and reverse ends).