Hi community!!! I am working with 16S sequence data in MOTHUR.
Initially I had 526345 sequences. After all “screen.seqs” and “remove.seqs” steps when I was heading for “classify.seqs” step I was having around 406528 sequences. The rests were removed in each quality screening and chimera removal steps.
initially, # of unique seqs: 172219 and total # of seqs: 526345
after preclustering, # of unique seqs: 94052 and total # of seqs: 526345
after chimera removal, # of unique seqs: 50148 and total # of seqs: 406528
Is such reduction in sequence numbers normal or I am doing something wrong?
On a separate set of sequence I startted with 671453 sequences. Before chimera removal, I had 605417 sequences.After chimera removal, the number of sequence reduced from 605417 to 450840. That implies I have lost total 33% sequences of which around 26% sequences lost during chimera removal. Is it normal also?
Also during the remove.lineage step 260 sequences from fasta file and 1573 sequneces from count file was removed. Please make a comment on it also?