pre.cluster drop of sequences...?

Commands in mothur
1

Hi There,
i just had a doubt regarding the pre.cluster…
In the Schloss example in the summary.seqs() after the pre.cluster you say you have now X number of unique seqeunces but that the total number of seqeunces is still the same:
mothur > summary.seqs(fasta=GQY1XT001.shhh.trim.unique.good.filter.unique.precluster.fasta, name=GQY1XT001.shhh.trim.unique.good.filter.unique.precluster.names)

Start End NBases Ambigs Polymer NumSeqs
Minimum: 1 449 244 0 3 1
2.5%-tile: 1 449 251 0 4 1694
25%-tile: 1 449 254 0 4 16937
Median: 1 449 255 0 4 33874
75%-tile: 1 449 255 0 4 50810
97.5%-tile: 1 449 255 0 6 66053
Maximum: 2 449 261 0 8 67746
Mean: 1.00006 449 254.103 0 4.3462

of unique seqs: 6831

total # of seqs: 67746


...But I don't get that total # of sequences...and # unique sees...I just get:
Start End NBases Ambigs Polymer NumSeqs Minimum: 1 1026 212 0 3 1 2.5%-tile: 1 1026 237 0 4 300 25%-tile: 1 1026 266 0 5 2995 Median: 1 1026 270 0 5 5989 75%-tile: 1 1026 280 0 5 8983 97.5%-tile:1 1026 285 0 6 11677 Maximum: 1 1026 422 0 8 11976 Mean: 1 1026 269.224 0 4.98205 # of Seqs: 11976

Output File Name:
16S_ads_all.trim.rename.unique.good.filter.unique.precluster.summary

And…after my unique seqs I get a # Seqs:18233 …and just after the filtering I get # Seqs: 43255…
So I am not sure I should worry about it …?

Thanks
kim

2

You need to include the names file when you run summary.seqs - it’s not clear that you’re doing that. What is the exact summary.seqs command you are running?

3

Thanks Pat,
yes indeed I was just using the summary.seqs() without adding the fasta and names…It seems like this way the total# seqs given is the #of unique sequences…
instead of the real total # of sequences