SRNAfrag: a pipeline and suite of tools to analyze fragmentation in small RNA sequencing data.

ABSTRACT: Fragments derived from small RNAs such as small nucleolar RNAs are biologically relevant but remain poorly understood. To address this gap, we developed sRNAfrag, a modular and interoperable tool designed to standardize the quantification and analysis of small RNA fragmentation across various biotypes. The tool outputs a set of tables forming a relational database, allowing for an in-depth exploration of biologically complex events such as multi-mapping and RNA fragment stability across different cell types. In a benchmark test, sRNAfrag was able to identify established loci of mature microRNAs solely based on sequencing data. Furthermore, the 5' seed sequence could be rediscovered by utilizing a visualization approach primarily applied in multi-sequence-alignments. Utilizing the relationa

SUBMITTER: Nakatsu K 

PROVIDER: S-EPMC10796253 | biostudies-literature | 2023 Nov

REPOSITORIES: biostudies-literature