tailfindr: Alignment-free poly(A) length measurement for Oxford Nanopore RNA and DNA sequencing

Maximilian Krause; Adnan M. Niazi; Kornel Labun; Yamila N. Torres Cleuren; Florian S. Müller; Eivind Valen

To identify the signal corresponding to the poly(A) tails in RNA reads, the raw signal from ONT native RNA sequencing is extracted from the FAST5 files and z-normalised. Next, signal values above +3 and below -3 are truncated. The resulting processed raw signal is smoothened by a moving average filter (window size 400 samples; stride 1) in both directions separately. Both smoothened signal vectors are then merged by point-by-point maximum calculation. Next, the calculated smoothened signal is segmented into regions being above or below 0.3. The expected signal of the ONT adapter consists of one segment above and one segment below 0.3 in smoothened signal. The poly(A) tail immediately follows the Nanopore Adapter, thus the next segment in which the smoothened signal is above 0.3 is considered the poly(A) region, and the boundaries of this segment are considered the rough start and end of poly(A) tail (Fig. 1B) .