Initially i am facing problem in filtering where very less reads have passed the filter. But now after setting q20, 50-60% reads passed the filter but I don't know why very less reads have passed on merging.
Can anyone help me to find solution to this problem?
Here I am attaching the denoising-stats report. Also I am attaching the command below.
Looking at all this data your reads should overlap, so this is weird.
It seems like there is enough length in your sequence to overlap but for some reason they are not overlapping. The only thing I can think of is something went wrong in the demux step and its making it so your data is randomly assigned to sequences and therefore the forward and reverse reads are not really meant to go together? I am not exactly sure. Can you attach/dm me your demux.qzv so I could take a look that would be very appreciated.