Fig. 3
From: T3E: a tool for characterising the epigenetic profile of transposable elements using ChIP-seq data
Overview of the T3E workflow for TE families/subfamilies enrichment estimation. A Read mappings from ChIP-seq and input control libraries are used as input for T3E. Note that mapping must be performed with a tool able to report all read mappings, including those that are ambiguous. B T3E estimates a probability for each position in the genome from the distribution of read mappings for the input control library. C T3E samples reads according to the probabilities estimated in (B) to generate N input libraries that are used to compute a P-value and a Fold-Change (FC). Every simulated input library has the same size as the ChIP-seq sample. D Read mappings are counted for ChIP-seq sample and every simulated input library. The read mapping count associated with the Kth TE family/subfamily (CK) is given by the sum of the portions (percentages of the length) of the reads that map to each of its TE copies, each weighted by the ambiguity of the corresponding mapping. E The FC of the Kth TE family/subfamily is calculated as the ratio between the number of read mappings for the sample (CKSample) and the average number of read mappings across all N simulated input libraries (CKAvgBackground)