No reads passed the filter. trunc_len_f (280) or trunc_len_r (212) may be individually longer than read lengths, or trunc_len_f + trunc_len_r may be shorter than the length of the amplicon + 12 nucleotides (the length of the overlap). Alternatively, other arguments (such as max_ee or trunc_q) may be preventing reads from passing the filter.
See above for debug info.
I upload the qzv files in case it works for you. Thank you very much in advance. 2014_BR.qzv (308.3 KB)
Also, please let me know if I can provide other information!
This is odd since your quality plots look good to me. Sounds like the issue is coming at the filtering step and this is hard to troubleshoot without looking at the actual fastq files.
Can you give us a bit more information about your samples:
What is your target region
How long is the expected overlap region
Can you print a few lines of your FASTQ files?
Throwing the kitchen sink at this thing
What happens if you re-run the same thing but leave the max_ee parameters at the default 2?
If nothing changes, can you try running just your forward reads to see if we get anything passing the filter then?
I have tried leave the max_ee parameters at the default 2
I am going to try running just my forward reads to see if we get anything passing the filter. Thanks
