Entering edit mode
7.5 years ago
L. A. Liggett
▴
120
I am using bcbio.rnaseq to analyze my bcbio analysis, but am having some trouble specifying the 'formula'. I have 9 samples 3 biological replicates of each condition. How do I input this when calling bcbio-rnaseq? This is what I'm trying:
bcbio-rnaseq summarize /dir/bcbio-project-file.yaml -o human
The only output I get is:
WARNING: update already refers to: #'clojure.core/update in namespace: incanter.core, being replaced by: #'incanter.core/update
Usage: bcbio-rnaseq summarize bcbio-project-file.yaml
Options: -h, --help -f, --formula FORMULA Formula to use in model (example: ~ batch + condition) -d, --dexseq Run DEXSeq -o, --organism ORGANISM organism (mouse, human) -s,
--sleuth Run Sleuth