If I were to want to use the Silva templates to align the esophageal sequences, is there a way to use the bacteria and archaea templates simultaneously, and what would the corresponding cut-offs be to the end-points you provide when you run screen.seqs (204, 4456)? By the way, how do you arrive at the 4456 figure?
Thanks,
Mike
You could concatenate the two reference files together and rename it and then use that for your alignment. If you post your results from summary.seqs we can help you figure out the proper start/end positions.
Okeedoke, so, here’s my summary:
mothur > align.seqs(fasta=esophagus.fasta, reference=silva.archaea.bacteria.fast
a)
Reading in the silva.archaea.bacteria.fasta template sequences… DONE.
It took 48 to read 17253 sequences.
Aligning sequences from esophagus.fasta …
100
200
300
400
500
600
700
710
It took 18 secs to align 710 sequences.
Using esophagus.align as input file for the fasta parameter.
Using 1 processors.
Start End NBases Ambigs Polymer NumSeqs
Minimum: 1103 26918 831 0 4 1
2.5%-tile: 1120 26996 840 0 4 18
25%-tile: 1120 27585 855 0 5 178
Median: 1120 28439 865 0 5 356
75%-tile: 1120 28464 870 0 5 533
97.5%-tile: 1147 29691 900 5 7 693
Maximum: 2049 43058 1378 20 8 710
Mean: 1129.95 28186.9 864.996 0.478873 5.09296
Output File Names:
esophagus.summary
Gracias!
Mike
I’d suggest using start=1147 (probably should be 1120 if you went from left to right…) and end=26918
You want to choose a start number that is greater than where most of your sequences start or that corresponds to where your primer leaves off (again, for left to right). You want to choose an end number that is less than where most of your sequences end.
Pat