I was walking through polyester with some students yesterday and remembered something which I seem to forget every now and then about the behavior of
simulate_experiment. It's summarized in this closed issue:
If you give
simulate_experiment a transcript and set
reads_per_transcript=0 it will turn that 0 to a 1 here:
I always seem to remember this after playing around a bit, so it's never ended up in one of my simulation datasets. I always remove the desired unexpressed transcripts from the FASTA instead of putting 0s, as recommended in that issue, but I noticed that it's not mentioned in the vignette or man pages of polyester. I could see someone accidentally giving
simulated_experiment e.g. all the reference transcripts, and putting a 0 for a majority of them. They may be surprised to find they are expressing every transcript with one read.