tReasure: R-based GUI package analyzing tRNA expression profiles from small RNA sequencing data

Jin Ok Lee, Jiyon Chu, Gyuyeon Jang, Minho Lee, Yeun Jun Chung

Research output: Contribution to journalArticlepeer-review

2 Scopus citations

Abstract

Background: Recent deep sequencing technologies have proven to be valuable resources to gain insights into the expression profiles of diverse tRNAs. However, despite these technologies, the association of tRNAs with diverse diseases has not been explored in depth because analytical tools are lacking. Results: We developed a user-friendly tool, tRNA Expression Analysis Software Utilizing R for Easy use (tReasure), to analyze differentially expressed tRNAs (DEtRNAs) from deep sequencing data of small RNAs using R packages. tReasure can quantify individual mature tRNAs, isodecoders, and isoacceptors. By adopting stringent mapping strategies, tReasure supports the precise measurement of mature tRNA read counts. The whole analysis workflow for determining DEtRNAs (uploading FASTQ files, removing adapter sequences and poor-quality reads, mapping and quantifying tRNAs, filtering out low count tRNAs, determining DEtRNAs, and visualizing statistical analysis) can be performed with the tReasure package. Conclusions: tReasure is an open-source software available for download at https://treasure.pmrc.re.kr and will be indispensable for users who have little experience with command-line software to explore the biological implication of tRNA expression.

Original languageEnglish
Article number155
JournalBMC Bioinformatics
Volume23
Issue number1
DOIs
StatePublished - Dec 2022

Keywords

  • GUI R packages
  • Small RNA sequence
  • tRNA expression analysis

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