deletions | additions       diff --git a/Correcting read depth and GC.tex b/Correcting read depth and GC.tex  index b66e9bb..49d01c2 100644  --- a/Correcting read depth and GC.tex  +++ b/Correcting read depth and GC.tex 
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\subsubsection{Adjusting total read depth}  In RNA-seq experiments, a small number of highly expressed genes can account for a large fraction of mapped reads \cite{XXXXX}. reads.  Variation in the expression level of these genes can therefore have a large effect on the number of reads that map to all other genes. genes \cite{10.1007/s12064-012-0162-3}.  In ChIP-seq experiments, the fraction of reads that come from peaks varies between experiments, likely due to differences in the antibody efficacy. To account for this source of variation, we calculate an adjusted total read depth, $T^{*}_{i,j}$ for each region and individual. The adjusted read depth is defined by a quartic function of the total read depth (summed across individuals) for each target region. The coefficients of the quartic function are estimated using a maximum likelihood approach described below.