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.

[VoidandZero]

Hi, how well do you understand the progress, I got a problem about paired end align using bowtie2(2.5.4). When I align paired end data, the result file created from "--al-gz" has no items with the size of 20B though the log showed some reads are aligned.