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VSS: variance-stabilized signals for sequencing-based genomic signals

Faezeh Bayat,Maxwell W. Libbrecht

Published 2020 in bioRxiv

ABSTRACT

Motivation A sequencing-based genomic assay such as ChIP-seq outputs a real-valued signal for each position in the genome that measures the strength of activity at that position. Most genomic signals lack the property of variance stabilization. That is, a difference between 100 and 200 reads usually has a very different statistical importance from a difference between 1,100 and 1,200 reads. A statistical model such as a negative binomial distribution can account for this pattern, but learning these models is computationally challenging. Therefore, many applications—including imputation and segmentation and genome annotation (SAGA)—instead use Gaussian models and use a transformation such as log or inverse hyperbolic sine (asinh) to stabilize variance. Results We show here that existing transformations do not fully stabilize variance in genomic data sets. To solve this issue, we propose VSS, a method that produces variance-stabilized signals for sequencingbased genomic signals. VSS learns the empirical relationship between the mean and variance of a given signal data set and produces transformed signals that normalize for this dependence. We show that VSS successfully stabilizes variance and that doing so improves downstream applications such as SAGA. VSS will eliminate the need for downstream methods to implement complex mean-variance relationship models, and will enable genomic signals to be easily understood by eye. Contact maxwl@sfu.ca. Availability https://github.com/faezeh-bayat/Variance-stabilized-units-for-sequencing-based-genomic-signals.

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