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

. CC-BY-NC-ND 4.0 International license peer-reviewed) is the author/funder. It is made available under a . CC-BY-NC-ND 4.0 International license peer-reviewed) is the author/funder. It is made available under a The copyright holder for this preprint (which was not . https://doi.org/10.1101/588343 doi: bioRxiv preprint 2.2 | Poly(A) and poly(T) tail length can be estimated from ONT DNA sequencing data ONT native RNA sequencing is lower in both quantity and quality compared to cDNA sequencing approaches and relies on large amounts of starting material (500 ng of poly(A)-selected RNA, [33, 34] ). Therefore, cDNA sequencing approaches that retain the full-length poly(A) tail would enable studies where material is scarce as well as increase statistical power of poly(A) tail estimates. We thus aimed to expand tailfindr to operate on ONT DNA sequencing approaches as well. Since standard cDNA approaches result in double-stranded DNA, both poly(A) as well as poly(T) stretches are present in ONT sequencing reads. During cDNA sequencing both of these strands are threaded through the pore separately from 5' to 3' (Fig. 2A) . Indeed we observe homogenous stretches of raw signal both at the beginning (poly(T) tail) as well as at the end (poly(A) tail) of individual raw read sequences (example for poly(T)-containing read in Figure S3B ).