• Corpus ID: 222141512

A comprehensive overview of computational tools for RNA-seq analysis

@article{Deshpande2020ACO,
  title={A comprehensive overview of computational tools for RNA-seq analysis},
  author={Dhrithi Deshpande and Karishma Chhugani and Yutong Chang and Aaron Karlsberg and Caitlin Loeffler and Jinyang Zhang and Agata Muszyńska and Jeremy Rotman and Laura Tao and Lana S. Martin and Brunilda Balliu and Elizabeth Tseng and Eleazar Eskin and Fangqing Zhao and Pejman Mohammadi and Pawel P. Labaj and Serghei Mangul},
  journal={arXiv: Genomics},
  year={2020}
}
RNA-sequencing (RNA-seq) has become an exemplar technology in modern biology and clinical applications over the past decade. It has gained immense popularity in the recent years driven by continuous efforts of the bioinformatics community to develop accurate and scalable computational tools. RNA-seq is a method of analyzing the RNA content of a sample using the modern sequencing platforms. It generates enormous amounts of genomic data in the form of nucleotide sequences, known as reads. RNA-seq… 
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References

SHOWING 1-10 OF 264 REFERENCES

Advancing RNA-Seq analysis

New approaches for RNA-Seq analysis that capture genome-wide transcription and splicing in unprecedented detail are introduced, and a de novo assembly approach implemented in the ABySS software reduces the annotation problem to that of aligning full-length cDNAs, which is well handled by several algorithms.

Advanced Applications of RNA Sequencing and Challenges

Next-generation sequencing technologies have revolutionarily advanced sequence-based research with the advantages of high-throughput, high-sensitivity, and high-speed. RNA-seq is now being used…

SeqBuster, a bioinformatic tool for the processing and analysis of small RNAs datasets, reveals ubiquitous miRNA modifications in human embryonic cells

The application of SeqBuster to small-RNA datasets of human embryonic stem cells revealed that most miRNAs present different types of isomiRs, some of them being associated to stem cell differentiation.

RNA CoMPASS: A Dual Approach for Pathogen and Host Transcriptome Analysis of RNA-Seq Datasets

RNA CoMPASS is presented, a comprehensive RNA-seq analysis pipeline for the simultaneous analysis of transcriptomes and metatranscriptomes from diverse biological specimens that leverages existing tools and parallel computing technology to facilitate the analysis of even very large datasets.

RNA Sequencing and Analysis.

This article provides an introduction to RNA-Seq methods, including applications, experimental design, and technical challenges, and applies them to investigate different populations of RNA.

Differential expression in RNA-seq: a matter of depth.

This work analyzed how sequencing depth affects the detection of transcripts and their identification as differentially expressed, and proposed a novel approach--NOISeq--that differs from existing methods in that it is data-adaptive and nonparametric.

Discovering chimeric transcripts in paired-end RNA-seq data by using EricScript

A novel computational framework, named chimEric tranScript detection algorithm (EricScript), for the identification of gene fusion products in paired-end RNA-seq data is proposed and demonstrates that EricScript enables to achieve higher sensitivity and specificity than existing methods with noticeably lower running times.

Single-cell RNA sequencing technologies and bioinformatics pipelines

The available scRNA-seq technologies and the strategies available to analyze the large quantities of data produced will impact both basic and medical science, from illuminating drug resistance in cancer to revealing the complex pathways of cell differentiation during development.

PRADA: pipeline for RNA sequencing data analysis

PRADA is a flexible, modular and highly scalable software platform that provides many different types of information available by multifaceted analysis starting from raw paired-end RNA-seq data: gene expression levels, quality metrics, detection of unsupervised and supervised fusion transcripts, Detection of intragenic fusion variants, homology scores and fusion frame classification.

rMATS: Robust and flexible detection of differential alternative splicing from replicate RNA-Seq data

A new statistical model and computer program, replicate MATS (rMATS), designed for detection of differential alternative splicing from replicate RNA-Seq data, which uses a hierarchical model to simultaneously account for sampling uncertainty in individual replicates and variability among replicates.
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