trouble with align.seqs and silva.nr_v119.align reference

Commands in mothur
1

Hi there,

I am trying to run a LSU sample set, but after I do the align.seqs step- my sequences are 2 - 17 bps in length. Weird! On average after the previous unique.seqs step, my sequences are about 300 bp in length. Something funky is happening in the align step but I dont know how to approach this problem. Any help would be much much appreciated.


Best
2

as I have reflected on this, I wonder if the silva database is only SSU sequences? is there a pre-existing LSU alignment/ taxonomy reference formatted for mothur in existence? I couldnt find one off of the mothur wiki

3

Yes, it’s only SSU - sorry but you’ll have to track down a LSU reference. SILVA hosts them, so you can probably start there.