Hi, I am analyzing my 454 reads (V1-3 region) following the 454 mothur SOP.
I experienced some problems with align.seqs. Here is the command i used (I used a dataset with around 2000 reads as a test file):
mothur > align.seqs(fasta=test.unique.fasta,reference=silva.bacteria.fasta,processors=2)
After aligned, I got the results like this:
Start End NBases Ambigs Polymer NumSeqs
Minimum: -1 -1 0 0 1 1
2.5%-tile: 1044 1044 1 0 1 51
25%-tile: 1044 1071 5 0 2 503
Median: 43056 43116 11 0 2 1006
75%-tile: 43096 43116 15 0 2 1508
97.5%-tile: 43116 43116 23 0 3 1960
Maximum: 43116 43116 69 0 5 2010
Mean: 26581.9 26610.7 10.7557 0 1.92438
of Seqs: 2010
It seems only few bps were aligned. Even if I use the E.coli fasta as a reference read, I got similar results.
So what is the problem? Thanks.