How to merge the pair end sample for GBS analysis in TASSEL software?

Question

[mathavanbioinfo]

Dear sir/Madam

I am very new to GBS (genotype by sequencing) analysis, I have completed one test run for pair-end read samples, the output of the hapmap.txt text file is shown below figure,

each sample has two files in the hmp.txt for example S188_R1.clean.fq.gz, S188_R2.clean.fq.gz please advise me Is this analysis meaningful?, or else I have merged the paired sample in a single file and then run GBS