Journal
BIOINFORMATICS
Volume 36, Issue 9, Pages 2926-2928Publisher
OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/btaa011
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Funding
- American Heart Association Postdoctoral Fellowship [18POST33990082]
- National Institutes of Health [R01-DK118287, T32-HL007284, R35-GM128635]
- American Diabetes Association [1-19-IBS-105]
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aSummary: Nascent transcript measurements derived from run-on sequencing experiments are critical for the investigation of transcriptional mechanisms and regulatory networks. However, conventional mRNA gene annotations significantly differ from the boundaries of primary transcripts. New primary transcript annotations are needed to accurately interpret run-on data. We developed the primaryTranscriptAnnotation R package to infer the transcriptional start and termination sites of primary transcripts from genomic run-on data. We then used these inferred coordinates to annotate transcriptional units identified de novo. This package provides the novel utility to integrate data-driven primary transcript annotations with transcriptional unit coordinates identified in an unbiased manner. Highlighting the importance of using accurate primary transcript coordinates, we demonstrate that this new methodology increases the detection of differentially expressed transcripts and provides more accurate quantification of RNA polymerase pause indices.
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