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As expected, the slope at maximum read count was 0.140.
A minimum read count of 10 was required for a splice junction to be considered expressed, whereas the maximum read count for a junction to be considered not expressed was five; the gap is a conservative filtering criterion.
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Hence, the estimation of the hyperparameters from the data should allow to capture the background nucleosome distribution., i.e. uniformly distributed in the interval, where denotes the maximum read counts in the corresponding chromosome.
Read counts were then normalized by dividing by the total count of mapped reads for the sample and multiplying by the maximum total read count across all samples.
The maximum read-count-normalized DNase I tag density was then determined for each master list DHS in each sample.
STAT3 peak summits, defined as the local maxima of read counts within a peak, were mapped to the nearest RefSeq TSS, incorporating strandedness, using an in-house script.
We also observed that the maximum CS was achieved in both cell lines at a read count threshold of one.
For Figure 2, Figure 3C and Figure 1 figure supplement 3, both read counts and enrichment values for each sample were independently scaled by dividing the values at each base by the maximum value encountered among the displayed genes or gene groups across stages after normalizing for both read count and fragment size differences.
The read count error equals 5√N/N, which decreases as the read count increases and is negligible for large read counts.
The reads were normalized to the total read count.
(A) Protein abundance versus miRNA read count.
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