I am new to mothur and have walked through the MiSeq SOP as well as analysis, essentially I have 40 samples, each with a large filter sequences and a smaller filter sequences for each sample (20 samples per filter size). I know need to separate my final.fasta / final.count etc. into two groups and run the analysis on each filter size separately. Is there a way to do this so late in the stage? or do I need to keep these separated from the beginning. I see there is a split.group command but produces a final.fasta / final.count for every sample listed, when in the end I just need two final files (final.large_filter.fasta, etc. and final.small_filter.fasta)
Hello, nice name!
I have problems getting to what you want to exactly do. Usually, I use R (phyloseq) to split my groups after Mothur for downstream analysis.
Have a nice day
If you want fasta files, I’d suggest using
remove.groups to specify what samples you want. After running the command, you’ll need to rename the output file since they’ll write over themselves when you rerun the command