Description
Hi, while running bamCompare as
bamCompare --operation mean --effectiveGenomeSize 2913022398 --normalizeUsing BPM --binSize 50 -b1 sample1.bam -b2 sample2.bam -o sample-MEAN.bpm.bw
I got the error
'--normalizeUsing BPM' is only valid if you also use '--scaleFactorMethod None'! To prevent erroneous output, I will quit now.
so I ran it again adding --scaleFactorMethod None
as follows
bamCompare --operation mean --effectiveGenomeSize 2913022398 --normalizeUsing BPM --binSize 50 -b1 sample1.bam -b2 sample2.bam --scaleFactorMethod None -o sample-MEAN.bpm.bw
but got the error
usage: bamCompare -b1 treatment.bam -b2 control.bam -o log2ratio.bw
bamCompare: error: unrecognized arguments: --scaleFactorMethod None
reading the manual of bamCompare I found that the right argument is --scaleFactorsMethod
instead of --scaleFactorMethod
, note the extra s
in the first one.
Thanks for this great package