MOESM13 of Expression and epigenomic landscape of the sex chromosomes in mouse post-meiotic male germ cells

Additional file 13. a RPKM threshold determination. Reads were mapped to Ensembl Genes (in blue) and to intergenic regions (in red). By comparing the expression levels of exons and intergenic regions, the intersection of the density plots was used to determine the threshold value to consider a gene as expressed (in our study= 0.22). b The true number of expressed genes in each bin (black) was estimated from the observed numbers for Ensembl genes (blue, same as a) by multiplication of the latter by the false discovery rate. This estimate was converted to cumulative amount, and the false negative rate was estimated as a function of expression level using the formula described in [48]. c. Bins were converted to cumulative amounts of genes expressed above the expression levels for genes (cum_genes; blue) and controls (cum_background; red). A false discovery rate fdr (green) was calculated at each expression level as described in [48].