I currently have two datasets from two sequencing runs which have both been put separately through the Miseq SOP up till classify.seqs. I am now wanting to compare some of the samples from one run to some of the samples from the other.
I am presuming that to do this I will have to somehow extract the samples I’m interested in and merge them into one file. I also thought I would have to redo some of the commands so that similar sequences from the two runs would be clustered together properly.
However, I’m not completely sure which files I should be merging together to do this. Would combining the fasta files from just before preclusterring be the best idea? I’m also not completely sure which commands I would have to use for extracting/merging sequences and whether I would also have to merge anything other than the fasta files (count files etc.).
Can anyone help?