search

alyssafrazee / polyester

Bioconductor package "polyester", devel version. RNA-seq read simulator.
http://biorxiv.org/content/early/2014/12/12/006015
89 stars 51 forks source link

Simulate Reads Without Experiment? #78

Closed nmshahir closed 2 years ago

nmshahir commented 2 years ago

Amazing tool! Forgive me for the very simplistic question but is there any way to simulate an experiment without fold changes?

alyssafrazee commented 2 years ago

You can set all fold changes = 1!

nmshahir commented 2 years ago

So I tried that and get Error in simulate_experiment("chr22_small.fa", readlen = 90, meanmodel = TRUE, : object 'basemeans' not found

this is the code I'm running using the data provided in polyester simulate_experiment('chr22_small.fa',readlen=90,meanmodel=TRUE, num_reps=1, fold_changes=1, outdir='simulated_reads')

nmshahir commented 2 years ago

Update: figured it out! I needed to update R.