MOIRAI: a compact workflow system for CAGE analysis

The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression

(2012) T. Derrien et al.   GENOME RESEARCH

Landscape of transcription in human cells

(2012) Sarah Djebali et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

5′ end–centered expression profiling using cap-analysis gene expression and next-generation sequencing

(2012) Hazuki Takahashi et al.   Nature Protocols

Next-generation sequencing data interpretation: enhancing reproducibility and accessibility

(2012) Anton Nekrutenko et al.   NATURE REVIEWS GENETICS

Unamplified cap analysis of gene expression on a single-molecule sequencer

(2011) M. Kanamori-Katayama et al.   GENOME RESEARCH

SAMStat: monitoring biases in next generation sequencing data

(2010) T. Lassmann et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan

(2010) Charles Plessy et al.   NATURE METHODS

TagDust--a program to eliminate artifacts from next generation sequencing data

(2009) T. Lassmann et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Development of a DNA barcode tagging method for monitoring dynamic changes in gene expression by using an ultra high-throughput sequencer

(2008) Norihiro Maeda et al.   BIOTECHNIQUES