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Automating ChIP-seq Experiments to Generate Epigenetic Profiles on 10,000 HeLa Cells
Published on: December 10, 2014
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Benchmark study comparing liftover tools for genome conversion of epigenome sequencing data.
Phuc-Loi Luu1, Phuc-Thinh Ong2, Thanh-Phuoc Dinh3
1Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney 2010, New South Wales, Australia.
NAR Genomics and Bioinformatics
|February 12, 2021
Summary
Genome assembly conversion using liftover tools is crucial for epigenome data integration. A new guideline improves liftover accuracy by removing aberrant regions, ensuring robust genome conversion between reference assemblies.
Area of Science:
- Bioinformatics
- Genomics
- Epigenetics
Background:
- Reference genome assemblies are frequently updated, necessitating the conversion of existing epigenome data to newer versions.
- Coordinate conversion using 'liftover' is a cost-effective alternative to re-aligning sequence data for integrating and visualizing epigenomic information across different genome builds.
Purpose of the Study:
- To benchmark the performance of six common liftover tools for converting whole genome bisulphite sequencing (WGBS) and ChIP-sequencing (ChIP-seq) data between genome assemblies.
- To develop a guideline for improving the accuracy and robustness of liftover conversions.
Main Methods:
- Benchmarking six liftover tools (UCSC liftOver, rtracklayer::liftOver, CrossMap, NCBI Remap, flo, segment_liftover) using 43 WGBS and 366 ChIP-seq datasets.
- Evaluating conversion accuracy and identifying aberrant regions.
- Developing a three-step guideline to refine liftover results.
Main Results:
- High correlation was observed among the six tools for WGBS data conversion.
- segment_liftover demonstrated more reliable results than UCSC liftOver for ChIP-seq interval conversion.
- Certain genomic regions were found to be inconsistently converted across liftover tools.
Conclusions:
- Liftover is a rapid method for converting epigenome data between genome assemblies, but accuracy can vary.
- A developed three-step guideline enhances liftover accuracy by removing aberrant regions, ensuring more robust genome conversion for downstream analysis.
