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  Copy number normalization distinguishes differential signals driven by copy number differences in ATAC-seq and ChIP-seq

Su, D., Peters, M., Soltys, V., & Chan, Y. (submitted). Copy number normalization distinguishes differential signals driven by copy number differences in ATAC-seq and ChIP-seq.

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 Creators:
Su, D1, Author                 
Peters, M1, Author           
Soltys, V1, Author                 
Chan, YF1, Author                 
Affiliations:
1Chan Group, Friedrich Miescher Laboratory, Max Planck Society, ou_3008688              

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 Abstract: A common objective across ATAC-seq and ChIP-seq analyses is to identify differential signals across contrasted conditions. However, in differential analyses, the impact of copy number variation is often overlooked. Here, we demonstrated copy number differences among samples could drive, if not dominate, differential signals. To address this, we propose a pipeline featuring copy number normalization. By comparing the averaged signal per gene copy, it effectively segregates differential signals driven by copy number differences from other factors. Further applying it to Down syndrome, we unveiled distinct dosage-dependent and -independent changes on chromosome 21. Thus, we recommend normalization as a general approach.

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 Dates: 2024-04
 Publication Status: Submitted
 Pages: -
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 Rev. Type: -
 Identifiers: DOI: 10.1101/2024.04.11.588815
 Degree: -

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