Zipper plot: visualizing transcriptional activity of genomic regions.

ABSTRACT:

Background

Reconstructing transcript models from RNA-sequencing (RNA-seq) data and establishing these as independent transcriptional units can be a challenging task. Current state-of-the-art tools for long non-coding RNA (lncRNA) annotation are mainly based on evolutionary constraints, which may result in false negatives due to the overall limited conservation of lncRNAs.

Results

To tackle this problem we have developed the Zipper plot, a novel visualization and analysis method that enables users to simultaneously interrogate thousands of human putative transcription start sites (TSSs) in relation to various features that are indicative for transcriptional activity. These include publicly available CAGE-sequencing, ChIP-sequencing and DNase-sequencing datasets. Our method on

SUBMITTER: Avila Cobos F 

PROVIDER: S-EPMC5414305 | biostudies-literature | 2017 May

REPOSITORIES: biostudies-literature