tradis_comparison1
Bio-tradis: compares two experimental conditions using the method of dembek et al.
Usage
tradis_comparison [-h]
[-f]
[-t
read
cutoff]
[-o
outputfile.csv]
[-p
outputplot.pdf]
--controls
controls.txt
--conditions
conditions.txt
Overview
Compares two experimental conditions using the method of Dembek et al. mBio 2015. Read counts per gene are compared using edgeR. This analysis requires experimental replicates.
Options
Required Arguments:
-
--controls -
control libraries, generally growth in a permissive condition
-
--conditions -
libraries exposed to the experimental condition being compared
Optional Arguments:
-
-o -
output filename
-
-p -
output filename for diagnostic plots
-
-f -
enable filtering on minimum read counts
-
-t -
if
--filteris enabled, sets minimum read count necessary in one condition for a gene to be included in the comparison.
Releases
Unchanged in 4 releases since Debian 10 (Buster).