I would like to use DiscoSNP++ to obtain variants from paired-end reads of a sample. The fastq file of this specific sample has been trimmed from adapters, and in some cases the paired-end reads have been merged due to overlapping sequences. The merging tool (Adapter Removal) produced three files: the merged reads (equivalent to single-end reads), and the remaining R1 and R2 reads that did not overlap.
My question is: can I run a single analysis with DiscoSNP++ provinding the three types of files [option 1]? Or shall I run two analyses: one with the single-end reads (R1, R2), and the other with the pair-end reads (merged reads) [option 2]?