I am currently analysing 18 samples on MiSeq, which I followed the MiSeq tutorial.
First I made a stability.file and proceed to the the align.seqs step.
However, I used primers 27F/519R to target the V1-V3 region.
Therefore, should I use the customized silva.bacteria.fasta file as in the MiSeq SOP tutorial or should I use the silva.bactera.align file of version 119?
When I was aligning the 18 samples using the silva.bacteria.align file using a supercomputer, it still runs out of memory.
Should I try to use the one provided in the tutorial?
Sorry if the question is unclear.