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One of the\nchallenges for primary transcript detection concerns the\nsimultaneous transcription of closely spaced genes, which needs\nto be properly divided into individually transcribed units. The\nR package transcriptR combines RNA-seq data with ChIP-seq data\nof histone modifications that mark active Transcription Start\nSites (TSSs), such as, H3K4me3 or H3K9/14Ac to overcome this\nchallenge. The advantage of this approach over the use of, for\nexample, gene annotations is that this approach is data driven\nand therefore able to deal also with novel and case specific\nevents. 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