I posted a similar question to this in a previous post (Pulling out specific sequences), but thought I would start a fresh thread for the second part of the question.
I have used the get.lineage command to pull out sequences classified as enterobacteriaceae and campylobacteriaceae and as a result, a .fasta file was obtained with sequences from all of my samples. However, I would like to focus only on 3 specific samples rather than the whole dataset (containing 100 samples).
Does anyone have any recommendations on how I can generate these .fasta files again, which only include data from individual samples?
Many thanks in advance,