Aligning multiple Fastq files using Bowtie2

Question

[deepak18]

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.

[deepak18]

Also if it is possible then how can I get multiple SAM output files each corresponding to one sample.

Answer 1

[WouterDeCoster]

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.

[deepak18]

Thank you for your valuable reply.