SeqOthello: querying RNA-seq experiments at scale

Ye Yu; Jinpeng Liu; Xinan Liu; Yi Zhang; Eamonn Magner; Erik Lehnert; Chen Qian; Jinze Liu

doi:10.1186/s13059-018-1535-9

SeqOthello: querying RNA-seq experiments at scale

Ye Yu, Jinpeng Liu, Xinan Liu, Yi Zhang, Eamonn Magner, Erik Lehnert, Chen Qian, Jinze Liu

Research output: Contribution to journal › Article › peer-review

30 Scopus citations

Abstract

We present SeqOthello, an ultra-fast and memory-efficient indexing structure to support arbitrary sequence query against large collections of RNA-seq experiments. It takes SeqOthello only 5 min and 19.1 GB memory to conduct a global survey of 11,658 fusion events against 10,113 TCGA Pan-Cancer RNA-seq datasets. The query recovers 92.7% of tier-1 fusions curated by TCGA Fusion Gene Database and reveals 270 novel occurrences, all of which are present as tumor-specific. By providing a reference-free, alignment-free, and parameter-free sequence search system, SeqOthello will enable large-scale integrative studies using sequence-level data, an undertaking not previously practicable for many individual labs.

Original language	English
Article number	167
Journal	Genome Biology
Volume	19
Issue number	1
DOIs	https://doi.org/10.1186/s13059-018-1535-9
State	Published - Oct 19 2018

Bibliographical note

Publisher Copyright:
© 2018 The Author(s).

Keywords

Compression
Gene fusion
Othello
Pan-cancer
Query
RNA-seq
SeqOthello
TCGA

ASJC Scopus subject areas

Ecology, Evolution, Behavior and Systematics
Genetics
Cell Biology

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1186/s13059-018-1535-9

Cite this

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abstract = "We present SeqOthello, an ultra-fast and memory-efficient indexing structure to support arbitrary sequence query against large collections of RNA-seq experiments. It takes SeqOthello only 5 min and 19.1 GB memory to conduct a global survey of 11,658 fusion events against 10,113 TCGA Pan-Cancer RNA-seq datasets. The query recovers 92.7% of tier-1 fusions curated by TCGA Fusion Gene Database and reveals 270 novel occurrences, all of which are present as tumor-specific. By providing a reference-free, alignment-free, and parameter-free sequence search system, SeqOthello will enable large-scale integrative studies using sequence-level data, an undertaking not previously practicable for many individual labs.",

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AU - Zhang, Yi

AU - Magner, Eamonn

AU - Lehnert, Erik

AU - Qian, Chen

AU - Liu, Jinze

PY - 2018/10/19

Y1 - 2018/10/19

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KW - Gene fusion

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KW - Query

KW - RNA-seq

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SeqOthello: querying RNA-seq experiments at scale

Abstract

Bibliographical note

Keywords

ASJC Scopus subject areas

UN SDGs

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