Fig. 2
From: Tools and best practices for retrotransposon analysis using high-throughput sequencing data
Comparison of the methods for the quantification of mouse retrotransposon families. a Comparison of the estimated abundance versus the true abundance for different quantification methods using mouse simulated TE-derived library. An R-squared value (R2) was calculated to evaluate the correlation of estimated values between simulated values b Comparison of the estimated abundance versus the true abundance for TEtools and when randomly reported reads are used for the TE quantification with FeatureCounts (FeatureCounts Random alignments). A PE genome-wide library (10X coverage) was simulated using the mouse genome with STAR for the mapping