Hi all,
I have working with my data and I think I have found a problem. Everything works well until filter.seqs command, that gives me the expected file, withour “…”. However, after doing unique.seqs I get a file were “.” appears in the alignment. I am using mothur 1.32.1. I have removed the “…” from final.fasta with a new filter.seqs and then I did a ML tree with fasttree and phylo.diversity, which gave me similar values (in fact there are not any effect of experimental treatmen of phylogenetic alpha-diversity). It seems that unique.seqs changes “–” into “…”, is it normal?This happens with several sequences.
HZSC42M02ISVNC #### sequence after filter.seqs
–C-T-AC-C-A-A-GG-CGACGA
HZSC42M02ISVNC #### sequence after unique.seqs
…C-T-AC-C-A-A-GG-CGACGA
I paste below the results from filter.seqs and unique.seqs: summary.seqs(fasta=andrei.unique.good.good.filter.fasta, name=andrei.good.good.names, processors=8)
Using 8 processors.
Start End NBases Ambigs Polymer NumSeqs
Minimum: 1 478 221 0 3 1
2.5%-tile: 1 478 226 0 4 1645
25%-tile: 1 478 231 0 4 16447
Median: 1 478 252 0 5 32893
75%-tile: 1 478 252 0 5 49339
97.5%-tile: 1 478 252 0 6 64140
Maximum: 3 478 273 0 7 65784
Mean: 1.00012 478 244.139 0 4.93173
of unique seqs: 8601
total # of seqs: 65784
summary.seqs(fasta=andrei.unique.good.good.filter.unique.fasta, name=andrei.unique.good.good.filter.names, processors=8)
Using 8 processors.
Start End NBases Ambigs Polymer NumSeqs
Minimum: 1 478 221 0 3 1
2.5%-tile: 1 478 226 0 4 1645
25%-tile: 1 478 231 0 4 16447
Median: 1 478 252 0 5 32893
75%-tile: 1 478 252 0 5 49339
97.5%-tile: 1 478 252 0 6 64140
Maximum: 3 478 273 0 7 65784
Mean: 1.00012 478 244.139 0 4.93173
of unique seqs: 7585
total # of seqs: 65784