To generate the TPM files as input for eqtl_prepare_expression.py, we used effective length (equation (6)). For genes and exons, we calculated effective length (equation (7)) using mean insert size from the Picard tools CollectInsertSizeMetrics tool (v.2.20.1; broadinstitute.github.io/picard/). For junctions, we fixed the effective length at 100. After calculating the effective length, we dropped any feature with an effective length less than or equal to one:6\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${\mathrm{TPM}}=1e6\times \frac{{\mathrm{Count}}/{\mathrm{effective}}\,{\mathrm{length}}}{\varSigma\,({\mathrm{count}}/{\mathrm{effective}}\,{\mathrm{length}})}$$\end{document}TPM=1e6×Count/effectivelengthΣ(count/effectivelength)7\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${\mathrm{Effective}}\,{\mathrm{length}}={\mathrm{length}}-({\mathrm{mean}}\,{\mathrm{insert}}\,{\mathrm{size}})+1$$\end{document}Effectivelength=length−(meaninsertsize)+1
