Merging datasets (miseq)


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?



You’ll likely want to go back to your files file and start again. You can merge the files file and just proceed as you did before.