I’ve been running chimera.uchime on 16S V4-V5 data for almost a week. Finally it’s done but when I try to remove the chimeras it gives me this warning:
[WARNING]: We found more than 25% of the bases in sequence .0000 to be ambiguous. Mothur is not setup to process protein sequences.
Removed 0 sequences from your fasta file.
In the log file I found that chime detected ~45% of chimeras. Is there a way to find if it’s real or something is wrong?
Here is summary of the data after pre clustering step:
Start End NBases Ambigs Polymer NumSeqs
Minimum: 1 805 335 0 3 1
2.5%-tile: 1 805 367 0 4 174017
25%-tile: 1 805 367 0 4 1740168
Median: 1 805 367 0 4 3480336
75%-tile: 1 805 370 0 5 5220504
97.5%-tile: 1 805 371 0 6 6786655
Maximum: 2 805 395 0 8 6960671
Mean: 1 805 368.379 0 4.37955
of unique seqs: 1583202
total # of seqs: 6960671