Why might I be getting differences in sequence lengths from those stipulated in the sop when I align, screen and filter the sequences?
mothur > align.seqs(fasta=esophagus.fasta, reference=core_set_aligned.imputed.fa
sta)
Reading in the core_set_aligned.imputed.fasta template sequences… DONE.
It took 1 to read 4938 sequences.
Aligning sequences from esophagus.fasta …
100
200
300
400
500
600
700
710
It took 15 secs to align 710 sequences.
Output File Names:
esophagus.align
esophagus.align.report
mothur > summary.seqs(fasta=esophagus.align)
Start End NBases Ambigs Polymer NumSeqs
Minimum: 131 4456 831 0 4 1
2.5%-tile: 185 4477 840 0 4 18
25%-tile: 187 4512 855 0 5 178
Median: 187 4532 865 0 5 356
75%-tile: 187 4554 870 0 5 533
97.5%-tile: 204 4610 900 5 7 693
Maximum: 486 6720 1378 20 8 710
Mean: 190.67 4538.28 864.996 0.478873 5.09296
of Seqs: 710
Output File Names:
esophagus.summary
mothur > screen.seqs(fasta=esophagus.align, group=esophagus.groups, start=204, end=4456, maxambig=5)
Output File Names:
esophagus.good.align
esophagus.bad.accnos
esophagus.good.groups
summary.seqs(fasta=esophagus.good.align)
mothur > summary.seqs(fasta=esophagus.good.align)
Using 1 processors.
Start End NBases Ambigs Polymer NumSeqs
Minimum: 131 4470 840 0 4 1
2.5%-tile: 182 4477 840 0 4 17
25%-tile: 187 4512 857 0 5 170
Median: 187 4532 866 0 5 339
75%-tile: 187 4554 870 0 5 508
97.5%-tile: 190 4609 900 2 7 661
Maximum: 204 4664 907 5 8 677
Mean: 187.1 4533.87 864.326 0.249631 5.09749
of Seqs: 677
Output File Names:
esophagus.good.summary
filter.seqs(fasta=esophagus.good.align, trump=., vertical=T)
Length of filtered alignment: 1046
Number of columns removed: 6636
Length of the original alignment: 7682
Number of sequences used to construct filter: 677
Output File Names:
esophagus.filter
esophagus.good.filter.fasta
Thanks,
Mike