deletions | additions       diff --git a/Correcting read depth and GC.tex b/Correcting read depth and GC.tex  index 8980917..d5eac0f 100644  --- a/Correcting read depth and GC.tex  +++ b/Correcting read depth and GC.tex 
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\subsection{Correcting for GC content and other effects on expected read depth}  Since the number of mapped reads can differ between sequencing lanes and runs, we initially model the expected number of counts, $\lambda_{hi}$, as a linear function of the total number of mapped reads for each individual, $T_i$. However, technical variation between experiments can change this relationship and reduce the power to detect true differences in read depths between samples or cause spurious associations. We directly model some known sources of technical variation and estimate adjusted total read depths, $T^{*}_{i,j}$, $T^{*}_{ij}$,  for each individual and target region. This gives us a more accurate estimate of the expected number of reads and boosts our ability to detect true QTLs. \subsubsection{Adjusting total read depth}