I am going through the tutorial of the Trimming. For pair-end trimming, swap the order of the two fastq input file of the forward and reverse end and trimming using exact same parameters resulted in a big change in the number of bases trimmed away. Could anyone explain why that is the case?
Do you mean that you entered the reverse reads where the forward read usually go, and forward as the reverse?
That will break the logic of many tools. The tool expects the reads to be in a certain orientation with respect to each other, and with respect to the genome they are based on.
I’m not sure how to explain this differently, but can let you know that odd results are expected from any tool if you provide odd inputs.
If someone else wants to jump in and add more, please do!