I'm new to using megan and have some paired-read data I want to look at. I've aligned reads using diamond, and I'm importing the .daa files. If I use the R1 file, specify paired reads then the message window tells me it's found 207 pairs, then gives me Reads=382,661, Assigned = 382,644. If I use the R2 file then it says 135 pairs, Reads = 359633, Assigned = 359611.
Have I misunderstood the paired reads function - surely it should give the same no matter which file you've told it to import?