deepTools consists of several command line and Galaxy wrappers for summarizing the information of Next Generation Sequencing data that can be mapped to a reference genome. Through the API, the engine powering the deepTools commands can be used for other purposes as well.
Our deepTools API example explains step-by-step how to make use of some deepTools modules to achieve analyses outside the scope of the deepTools suite such as counting reads for certain genome regions and computing the FRiP score.
Complete information can be found in the following links: Index and Module Index
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