Additional file 3.
Peak and transcript detection as a function of read depth. (a) Increasing the number of aligned reads sampled from three different aligners (BWA, GSNAP and TopHat 2) shows an increased peak detection (linear regression R2 = 0.83). Reads were sampled from aligned reads of the MeRIP-seq HEK293T sample 2 dataset. (b) The number of transcripts that contain peaks for each of the subsampled levels. While increasing the read depth results in a dramatic increase in the number of peaks, the number of transcripts shows a much slower increase, indicating that increasing the read depth likely finds peaks with lower m6A stoichiometry.
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Saletore et al. Genome Biology 2012 13:175 doi:10.1186/gb-2012-13-10-175