Error: unrecognized arguments using deepTools bamCoverage
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!
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