Hi, I am just curious. Can we use STAR aligner to align the paired-end reads as a single-end? What are the consequences of the output of such alignment?
Yes, STAR can align paired-end reads as single-end, just run STAR two times, one with `--readFilesIn
 R1.fastq`, another with `--readFilesIn R2.fastq`.

> What are the consequences of the output of such alignment?

First and foremost, the mapped reads will be considered as single-end. In addition, the proportion of multi-mappers may increase.