CoCo: RNA-seq read assignment correction for nested genes and multimapped reads

Simultaneous sequencing of coding and noncoding RNA reveals a human transcriptome dominated by a small number of highly expressed noncoding genes

(2018) Vincent Boivin et al.   RNA

Protein coding genes as hosts for noncoding RNA expression

(2018) Vincent Boivin et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Characterizing Expression and Processing of Precursor and Mature Human tRNAs by Hydro-tRNAseq and PAR-CLIP

(2017) Tasos Gogakos et al.   Cell Reports

RNA-seq of human reference RNA samples using a thermostable group II intron reverse transcriptase

(2016) Ryan M. Nottingham et al.   RNA

RNA-Seq methods for transcriptome analysis

(2016) Radmila Hrdlickova et al.   Wiley Interdisciplinary Reviews-RNA

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

GtRNAdb 2.0: an expanded database of transfer RNA genes identified in complete and draft genomes

(2015) Patricia P. Chan et al.   NUCLEIC ACIDS RESEARCH

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

(2015) Nuala A. O'Leary et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2016

(2015) Andrew Yates et al.   NUCLEIC ACIDS RESEARCH

High-throughput sequencing of human plasma RNA by using thermostable group II intron reverse transcriptases

(2015) Yidan Qin et al.   RNA

A resource of ribosomal RNA-depleted RNA-Seq data from different normal adult and fetal human tissues

(2015) Jocelyn Y.H. Choy et al.   Scientific Data

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Identification of discrete classes of small nucleolar RNA featuring different ends and RNA binding protein dependency

(2014) Gabrielle Deschamps-Francoeur et al.   NUCLEIC ACIDS RESEARCH

Diverse modes of evolutionary emergence and flux of conserved microRNA clusters

(2014) Jaaved Mohammed et al.   RNA

The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote

(2013) Yang Liao et al.   NUCLEIC ACIDS RESEARCH

Insights into snoRNA biogenesis and processing from PAR-CLIP of snoRNA core proteins and small RNA sequencing

(2013) Shivendra Kishore et al.   GENOME BIOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

MicroRNA Sequence and Expression Analysis in Breast Tumors by Deep Sequencing

(2011) T. A. Farazi et al.   CANCER RESEARCH

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

RNA-Seq gene expression estimation with read mapping uncertainty

(2009) Bo Li et al.   BIOINFORMATICS

A rescue strategy for multimapping short sequence tags refines surveys of transcriptional activity by CAGE

(2008) Geoffrey J. Faulkner et al.   GENOMICS

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS