I have a pair end SRA files for which I have done FASTQc. The SRA files are then mapped against the reference sequence using Bowtie2. While mapping the paired ends with the reference sequence using Bowtie2 tool of galaxy, I have set an option of writing unaligned reads and aligned reads in separate files. The output, I have got are 2 unaligned reads in fastqsanger format (L and R), one aligned read in fastqsanger and one sorted aligned reads in bam format.
I used sorted aligned reads for further analysis, but to check the unaligned reads what process should I follow?
Now how do I further interpret the results of unaligned reads?
Is this procedure is fine to analyze the unaligned reads or do I need to check the unaligned read in other way?