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DNA sequencing is used for far more than actually reading the DNA sequence. The advent of massive parallel DNA sequencing (synonyms: shotgun sequencing, next-generation sequencing, deep sequencing) has enabled researchers to do quantitative counting of RNA and DNA molecules, which can be combined with more spophisticated biochemical set-ups allowing the interrogation of active transcription (RNA-seq, PRO-seq, GRO-seq) as well as egpigenetic DNA modifications (bisulfite sequencing), insights about protein-DNA interactions and histone mark distributions (ChIP-seq), the 3D structure of chromatin (ChIA-PET, ChIP-seq), and many more. Even antibody-stainings typically used for FACS analyses can now be translated into DNA reads (CITE-seq).
The figure above taken from Frese et al., 2013, highlights some of the most commonly applied seq-based applications. For more details about the different high-throughput sequencing platforms and applications, see Goodwin et al., 2016 and Reuter et al., 2015.
