Hei,
I notice that after I run the shhh.flows command followed by trim.seqs, the length of the reads reduced (supposed to be 400bp/Titanium) (A) compare to run the trim.seqs directly without (B). What could it be?
A. mothur > trim.flows(flow=Batch.flow, oligos=Batch.oligos, pdiffs=2, bdiffs=1,processors=2)
mothur > shhh.flows(file=Batch.flow.files,processors=2)
mothur > trim.seqs(fasta=Batch.flow.shhh.fasta, name=Batch.flow.shhh.names, oligos=Batch.oligos, pdiffs=2, bdiffs=1,
maxhomop=8, minlength=200, flip=F, processors=2)
Start End NBases Ambigs Polymer NumSeqs Minimum: 1 233 233 0 3 1 2.5%-tile: 1 247 247 0 3 4223 25%-tile: 1 257 257 0 4 42229 Median: 1 264 264 0 5 84457 75%-tile: 1 269 269 0 5 126685 97.5%-tile: 1 280 280 0 7 164691 Maximum: 1 312 312 0 8 168913 Mean: 1 263.143 263.143 0 4.89363 # of unique seqs: 71408 total # of seqs: 168913
B. mothur > trim.seqs(fasta=Batch.Fasta, name=Batch.names, oligos=Batch.oligos, pdiffs=2, bdiffs=1, qwindowaverage=25, qwindowsize=50, maxhomop=8, minlength=200, flip=F, processors=2)
Start End NBases Ambigs Polymer
Minimum: 1 250 250 0 3
2.5%-tile: 1 258 258 0 4
25%-tile: 1 359 359 0 5
Median: 1 392 392 0 5
75%-tile: 1 424 424 0 5
97.5%-tile: 1 492 492 0 7
Maximum: 1 536 536 0 8
Many thanks!!