FeatureCounts is a highly efficient general-purpose read summarizing program that counts mapped reads to genomic features such as genes, exons, promoter, gene bodies, genomic bins and chromosomal locations.
It can be used to count both RNA-seq and genomic DNA-seq reads.
FeatureCounts takes as input SAM/BAM files and an annotation file including chromosomal coordinates of features. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features.
For more details, see: Liao et al, Bioinformatics 2013; doi: 10.1093/bioinformatics/btt656
featureCounts: an efficient general purpose program for assigning sequence reads to genomic features
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