I want to align multiple paired end Fastq files belonging to different samples (RNA-seq reads) using Bowtie2. Bowtie allows alignment for multiple Fastq files at once but produces only one output SAM file specified by -S flag. I wanted to know whether this output file would be useful for downstream applications. Thanks.
As far as I know, no, it's not possible to have multiple samples/fastq files result in multiple sam/bam files (or add different read groups). Why would you want to do this?
Just run bowtie separately for each sample. Don't make this more complicated than necessary.