Systematic evaluation of spliced alignment programs for RNA-seq data
Pär G. Engström,Tamara Steijger,Botond Sipos,Gregory R. Grant,André Kahles,André Kahles,Gunnar Rätsch,Gunnar Rätsch,Nick Goldman,Tim Hubbard,Jennifer Harrow,Roderic Guigó,Paul Bertone +12 more
TLDR
A comparison of 26 mapping protocols based on 11 programs and pipelines found major performance differences between methods on numerous benchmarks, including alignment yield, basewise accuracy, mismatch and gap placement, exon junction discovery and suitability of alignments for transcript reconstruction.Abstract:
High-throughput RNA sequencing is an increasingly accessible method for studying gene structure and activity on a genome-wide scale. A critical step in RNA-seq data analysis is the alignment of partial transcript reads to a reference genome sequence. To assess the performance of current mapping software, we invited developers of RNA-seq aligners to process four large human and mouse RNA-seq data sets. In total, we compared 26 mapping protocols based on 11 programs and pipelines and found major performance differences between methods on numerous benchmarks, including alignment yield, basewise accuracy, mismatch and gap placement, exon junction discovery and suitability of alignments for transcript reconstruction. We observed concordant results on real and simulated RNA-seq data, confirming the relevance of the metrics employed. Future developments in RNA-seq alignment methods would benefit from improved placement of multimapped reads, balanced utilization of existing gene annotation and a reduced false discovery rate for splice junctions.read more
Citations
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Journal ArticleDOI
HISAT: a fast spliced aligner with low memory requirements
TL;DR: Tests showed that HISAT is the fastest system currently available, with equal or better accuracy than any other method, and requires only 4.3 gigabytes of memory.
Journal ArticleDOI
A survey of best practices for RNA-seq data analysis
Ana Conesa,Pedro Madrigal,Pedro Madrigal,Sonia Tarazona,David Gomez-Cabrero,Alejandra Cervera,Andrew McPherson,Michał Wojciech Szcześniak,Daniel J. Gaffney,Laura L. Elo,Xuegong Zhang,Ali Mortazavi +11 more
TL;DR: All of the major steps in RNA-seq data analysis are reviewed, including experimental design, quality control, read alignment, quantification of gene and transcript levels, visualization, differential gene expression, alternative splicing, functional analysis, gene fusion detection and eQTL mapping.
Journal ArticleDOI
The R package Rsubread is easier, faster, cheaper and better for alignment and quantification of RNA sequencing reads.
TL;DR: Rsubread is presented, a Bioconductor software package that provides high-performance alignment and read counting functions for RNA-seq reads that integrates read mapping and quantification in a single package and has no software dependencies other than R itself.
Journal ArticleDOI
RNA sequencing: the teenage years
TL;DR: Advances in RNA-sequencing technologies and methods over the past decade are discussed and adaptations that are enabling a fuller understanding of RNA biology are outlined, from when and where an RNA is expressed to the structures it adopts.
Journal ArticleDOI
Resetting Transcription Factor Control Circuitry toward Ground-State Pluripotency in Human
Yasuhiro Takashima,Ge Guo,Remco Loos,Jennifer Nichols,Gabriella Ficz,Felix Krueger,David Oxley,Fátima Santos,James Clarke,William Mansfield,Wolf Reik,Paul Bertone,Paul Bertone,Austin Smith +13 more
TL;DR: It is reported that short-term expression of two components, NANOG and KLF2, is sufficient to ignite other elements of the network and reset the human pluripotent state and demonstrate feasibility of installing and propagating functional control circuitry for ground-state pluripotency in human cells.
References
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