cleanUpdTSeq: This package classifies putative polyadenylation sites.

In jianhong/cleanUpdTSeq: cleanUpdTSeq cleans up artifacts from polyadenylation sites from oligo(dT)-mediated 3' end RNA sequending data

This package classifies putative polyadenylation sites.

Description

3'ends of transcripts have generally been poorly annotated. With the advent of deep sequencing, many methods have been developed to identify 3'ends. The majority of these methods use an oligodT primer which can bind to internal adenine-rich sequences, and lead to artifactual identification of polyadenylation sites. Heuristic filtering methods rely on a certain number of As downstream of a putative polyadenylation site to classify the site as true or oligodT primed. This package provides a robust method to classify putative polyadenylation sites using a Naive Bayes classifier.

Author(s)

Sarah Sheppard, Haibo Liu, Jianhong Ou, Nathan Lawson, Lihua Julie Zhu

jianhong/cleanUpdTSeq documentation built on Oct. 27, 2023, 2:14 p.m.