What to keep after a full run?

Let’s say I start with a dataset of fastq files, stability.files and a script to automate a Mothur MiSeq SOP from start to finish. It finishes. No errors – yay!

Quick question: do I need to keep all the “stability.trim…” files that were generated? I certainly will keep the dist files, summary tables, count tables, and taxonomy tables generated at the end. But once I know my dataset processed properly, do I keep all the intermediate files?

Thanks in advance,

You probably don’t need to keep the intermediate files. I tend to keep these and just compress them so they don’t take up too much space. I usually find that I wish I had something that I accidentally deleted :slight_smile:


Thanks for that. I tend to do that now; even though hard drives are cheap I’m going through them!