ena-STUDY-Computational Biology Unit, University of Bergen-21-03-2019-13:03:47:965-34
tailfindr: Alignment-free poly(A) length measurement for Oxford Nanopore RNA and DNA sequencing
Background:Polyadenylation at the 3'-end is a major regulator of messenger RNA and its length is known to affect nuclear export, stability and translation, among others. Only recently, strategies have emerged that allow for genome-wide poly(A) length assessment. These methods identify genes connected to poly(A) tail measurements indirectly by short-read alignment to genetic 3'-ends. Concurrently Oxford Nanopore Technologies (ONT) established full-length isoform RNA sequencing that contains the entire poly(A) tail. However, assessing poly(A) length through basecalling has so far not been possible due the inability to resolve long homopolymeric stretches in ONT sequencing.We developed tailfindr: an R package to estimate poly(A) tail length on ONT long-read sequencing data. tailfindr operates on unaligned, basecalled data. It measures poly(A) tail length from both native RNA and DNA sequencing, which for the first time makes poly(A) tail studies by full-length cDNA approaches possible. We assess tailfindr's performance across different poly(A) lengths, demonstrating that tailfindr is a versatile tool providing poly(A) tail estimates across a wide range of conditions.What does this dataset contain:The data presented here was used test tailfindr's performance on ONT 1D RNA and DNA reads containing tail lengths of 10, 30, 40, 60, 100, and 150 nt.Number of replicates present:Both RNA and DNA datasets have two replicates each.Basecalling details:- Both RNA and DNA raw reads were basecalled using Albacore v2.3.3.- Additionally, DNA raw reads were basecalled with Guppy v2.3.1 flipflop model as well.
Background:Polyadenylation at the 3'-end is a major regulator of messenger RNA and its length is known to affect nuclear export, stability and translation, among others. Only recently, strategies have emerged that allow for genome-wide poly(A) length assessment. These methods identify genes connected to poly(A) tail measurements indirectly by short-read alignment to genetic 3'-ends. Concurrently Oxford Nanopore Technologies (ONT) established full-length isoform RNA sequencing that contains the entire poly(A) tail. However, assessing poly(A) length through basecalling has so far not been possible due the inability to resolve long homopolymeric stretches in ONT sequencing.We developed tailfindr: an R package to estimate poly(A) tail length on ONT long-read sequencing data. tailfindr operates on unaligned, basecalled data. It measures poly(A) tail length from both native RNA and DNA sequencing, which for the first time makes poly(A) tail studies by full-length cDNA approaches possible. We assess tailfindr's performance across different poly(A) lengths, demonstrating that tailfindr is a versatile tool providing poly(A) tail estimates across a wide range of conditions.What does this dataset contain:The data presented here was used test tailfindr's performance on ONT 1D RNA and DNA reads containing tail lengths of 10, 30, 40, 60, 100, and 150 nt.Number of replicates present:Both RNA and DNA datasets have two replicates each.Basecalling details:- Both RNA and DNA raw reads were basecalled using Albacore v2.3.3.- Additionally, DNA raw reads were basecalled with Guppy v2.3.1 flipflop model as well.