Error: unrecognized arguments using deepTools bamCoverage

Question

[Daria]

Hello everyone!

I'm trying to visualize ChIP-seq data with deepTools but facing errors when use optional arguments for normalization.

Commands like:

bamCoverage -b file.bam -o file.bigWig -of bigwig --normalizeUsing RPGC --effectiveGenomeSize 2862010578 --ignoreForNormalization chrX chrY
bamCompare -b1 file-1.bam -b2 file-2.bam -o files-1-2.bigWig -of bigwig --normalizeUsing RPGC --effectiveGenomeSize 2862010578 --ignoreForNormalization chrX chrY

lead to the following messages:

bamCoverage: error: unrecognized arguments: C-17.bam RPGC --effectiveGenomeSize 2862010578
bamCompare: error: unrecognized arguments: RPGC --effectiveGenomeSize 2862010578

Both commands without --normalizeUsing RPGC --effectiveGenomeSize 2862010578 --ignoreForNormalization chrX chrY part works just fine. I have 2.5.7 version of deepTools.

Could someone help me with this problem? Any suggestions would be appreciated!

Thank you!