We are hoping to analyse a set of sequences that come from three different MiSeq runs. Sequences from the first two runs will have unique identifiers. However we are trying to find out if it will be possible to compare also a third run (which is a different species) if the same identifiers (barcodes) are used as in the second run (i.e. we are using the barcoded Caporaso reverse primers). If anyone can let me know if this is possible and if so what is the best way, that would be great.
Assuming they come from different sequencing runs you can just trim off the barcodes/primers then pool the resulting sequences.
So basically run trim.seqs on both raw sequence files, then combined the fasta/names/groups files with merge.files.
Great, many thanks for the reply.
Will I also still be able to compare individual samples between the two MiSeq runs (even though they had the same barcodes before trimming and pooling)?
Yep - as long as the samples have different group names you should be in good shape.
Great! That’s very good news.