featureCounts: an efficient general purpose program for assigning sequence reads to genomic features.
BACKGROUND
Next-generation sequencing technologies generate millions of short sequence reads, which are usually aligned to a reference genome. In many applications, the key information required for downstream analysis is the number of reads mapping to each genomic feature, for example to each exon or each gene. The process of counting reads is called read summarization. Read summarization is required for a great variety of genomic analyses but has so far received relatively little attention in the literature.


RESULTS
We present featureCounts, a read summarization program suitable for counting reads generated from either RNA or genomic DNA sequencing experiments. featureCounts implements highly efficient chromosome hashing and feature blocking techniques. It is considerably faster than existing methods (by an order of magnitude for gene-level summarization) and requires far less computer memory. It works with either single or paired-end reads and provides a wide range of options appropriate for different sequencing applications.


METHODS
featureCounts is available under GNU General Public License as part of the Subread (http://subread.sourceforge.net) or Rsubread (http://www.bioconductor.org) software packages.
Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Department of Computing and Information Systems and Department of Mathematics and Statistics, The University of Melbourne, Parkville, VIC 3010, Australia.
Yang
Y
Liao
Gordon K
GK
Smyth
Wei
W
Shi
D000465:Algorithms; D016678:Genome; D023281:Genomics / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing; D006657:Histones / Q000737:chemistry / Q000235:genetics; D017423:Sequence Analysis, RNA; D012984:Software
D006657:Histones