Difference between single and paired end align strategy in bowtie2

[c4-driod]

Hi, @BenLangmead, It's sorry to bother you. May I know the difference of data processing between single and paired end align in bowtie2 ? Which of them owns the larger reads utilization rate if I use the "fq1" for single align and "fq1" and "fq2" for paired align? I asked here since it's hard for me to find the answer in the source code. yours best, c4-driod.