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Total uniquely mapped tags were normalized to 10 million reads to generate tracks.
Tags were normalized among all libraries using the full quantile method from the EDAseq (Risso et al., 2011) package in Bioconductor.
All tags were normalized to tags per million (TPM) as described by Meyers et al [ 7].
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The TAG was normalized to total cellular protein.
TAG was normalized to total protein to control for differences in cell number or volume.
The abundance of each tag was normalized to one transcript per million (TPM) for between sample comparison purposes.
Datasets for different stages were normalized for the total number of uniquely mapped tags.
Tag counts were normalized to 100,000 tags per library.
To calculate average tag counts from reproducible peaks, tag counts were normalized to total mapped reads, and further ranked by tag counts.
Tag frequencies were normalized for library size by dividing the tag frequency by the total number of tags in the library multiplied by an arbitrary factor of 200,000.
Tag counts were normalized to the total number of tags counted per experiment and averaged for each experimental condition.
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