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?
HI I can follow what you have done. However it is a little unclear what biological question you are trying to answer so it is a little difficult to know how to help. can you elaborate at little? Guy
PS you might find running 'Flagstat tabulate descriptive stats for BAM datset' on your BAM file. This will tell you how many of your reads mapped and different ways they may have mapped