deeptools
how to calculate the signal within regions ignored when normalized?
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Dear deeptools developer,
I am using deeptools bamCoverage to convert bam files to bw files. To exclude the effect of gender (chrX), I used the argument --ignoreForNormalization chrX. What I don't understand is how deeptools calculate the normalized signal density within chrX since the chrX has been ignored?
I look forward to your reply! Many thanks in advance!! Yang
