Supporting data for "RED-ML: a novel, effective RNA editing detection method based on machine learning"

Dataset type: Software, Epigenomic
Data released on February 28, 2017

Hou Y; Lei M; Li Q; Li W; Liu D; Liu X; Lu H; Lu L; Ren S; Sun Y; Wang J; Wang Z; Wu L; Xia M; Xiong H; Xu L; Zhu S; Wu K; Yang H; Xu X; Lee LJ (2017): Supporting data for "RED-ML: a novel, effective RNA editing detection method based on machine learning" GigaScience Database. http://dx.doi.org/10.5524/100275

DOI10.5524/100275

With the advancement of second generation sequencing techniques, our ability to detect and quantify RNA editing on a global scale has been vastly improved. As a result, RNA editing is now being studied under a growing number of biological conditions so that its biochemical mechanisms and functional roles can be further understood. However, a major barrier that prevents RNA editing from being a routine RNA-seq analysis, similar to gene expression and splicing analysis for example, is the lack of user-friendly and effective computational tools.
Based on years of experience of analyzing RNA editing using diverse RNA-seq datasets, we have developed a software tool RED-ML: RNA Editing Detection based on Machine learning (pronounced as “red ML”). The input to RED-ML can be as simple as a single BAM file, while it can also take advantage of matched genomic variant information when available. The output not only contains detected RNA editing sites, but also a confidence score to facilitate downstream filtering. We have carefully designed validation experiments and performed extensive comparison and analysis to show the efficiency and effectiveness of RED-ML under different conditions, and it can accurately detect novel RNA editing sites without relying on curated RNA editing databases. We have also made this tool freely available via GitHub.
We have developed a highly accurate, speedy and general-purpose tool for RNA editing detection using RNA-seq data. With the availability of RED-ML, it is now possible to conveniently make RNA editing a routine analysis of RNA-seq. We believe this can greatly benefit the RNA editing research community and has profound impact to accelerate our understanding of this intriguing post-transcriptional modification process.

Additional details

Read the peer-reviewed publication(s):

Xiong, H., Liu, D., Li, Q., Lei, M., Xu, L., Wu, L., … Lee, L. J. (2017). RED-ML: a novel, effective RNA editing detection method based on machine learning. GigaScience, 6(5). doi:10.1093/gigascience/gix012

Additional information:

https://github.com/BGIRED/RED-ML

Accessions (data included in GigaDB):

BioProject: PRJNA373807

Accessions (data not in GigaDB):

SRA: SRP007605





Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
SAMN063191179606HumanhumanHomo sapiens Description:DNA extracted from CH24T
Alternative names:CH24T
Sex:not collected
...
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SAMN063191189606HumanhumanHomo sapiens Description:RNA extracted from CH24T
Alternative names:CH24T
Sex:not collected
...
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SAMN063191199606HumanhumanHomo sapiens Description:RNA extracted from CH24T
Alternative names:CH24T
Sex:not collected
...
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SAMN063191209606HumanhumanHomo sapiens Description:DNA extracted from CH62T
Alternative names:CH62T
Sex:not collected
...
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SAMN063191219606HumanhumanHomo sapiens Description:RNA extracted from CH62T
Alternative names:CH62T
Sex:not collected
...
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SAMN063191229606HumanhumanHomo sapiens Description:RNA extracted from CH62T
Alternative names:CH62T
Sex:not collected
...
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SAMN063191239606HumanhumanHomo sapiens Description:RNA extracted from YH
Alternative names:YH
Sex:not collected
...
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SAMN063191249606HumanhumanHomo sapiens Description:RNA extracted from Hela
Alternative names:Hela
Sex:not collected
...
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SAMN063191259606HumanhumanHomo sapiens Description:RNA extracted from Hela
Alternative names:Hela
Sex:not collected
...
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Displaying 1-9 of 9 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
SAMN06319117alignmentBAM166.32 GB2017-02-23
SAMN06319118alignmentBAM11.82 GB2017-02-23
SAMN06319119alignmentBAM7.22 GB2017-02-23
SAMN06319120alignmentBAM155.17 GB2017-02-23
SAMN06319121alignmentBAM8.49 GB2017-02-23
SAMN06319122alignmentBAM2.41 GB2017-02-23
MD5sumUNKNOWN0.95 KB2017-02-23
SAMN06319124alignmentBAM3.08 GB2017-02-23
SAMN06319125alignmentBAM19.41 GB2017-02-23
ReadmeTEXT2.35 KB2017-02-23
Displaying 1-10 of 18 File(s).
Date Action
February 28, 2017 Dataset publish
March 6, 2017 Manuscript Link added : 10.1093/gigascience/gix012