![]() ![]() To name a few prominent examples, ChIP-exo is a derivative of ChIP-seq where exonucleases are used to identify the genomic location of DNA-protein binding-sites with higher resolution. ![]() įurthermore, there are already numerous experimental protocols related to ChIP-seq available and new protocols are published all the time. For more in-depth information we recommend the “ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia”. For example, the ENCODE Project ( ENCyclopedia Of DNA Elements) has produced data on hundreds of regulatory factors (see ) in mouse and human. Usually a control experiment is performed where the immuno-precipitation step is left out or an antibody that is not specifically binding to the target genome is used. Following this Chromatin Immuno- Precipitation (ChIP) step, the short stretches of DNA attached to the protein of interest are identified by high-throughput sequencing.įor any targeted protein and a given cell-line or condition, this results in several million reads of raw sequencing data. After shearing the DNA, a protein of interest is extracted along with the cross-linked DNA fragments from the cell-lysate using specific antibodies. In broad terms, these techniques chemically cross-link proteins to those stretches of DNA they are bound to in vivo. These protocols provide us with a deeper understanding of gene-regulatory and epigenetic mechanisms by identifying, for example, Transcription-Factor Binding Sites (TFBS), open chromatin regions or the location of epigenetic marks. In order to identify functional elements in a genome, a number of experimental high-throughput techniques have been developed for investigating specific interactions between proteins and DNA. The results show that CLC shape-based peak caller ranks well among popular state-of-the-art peak callers while providing flexibility and ease-of-use. In order to show the applicability of the method to similar *-seq protocols, we also investigate algorithmic performances on DNase-seq data. Using independently validated benchmark datasets, we compare our implementation to other state-of-the-art algorithms explicitly designed to analyse ChIP-seq data and provide an evaluation in terms of receiver-operator characteristic (ROC) plots. Thanks to the generality of the idea and the fact the algorithm is able to learn the peak shape from the data, the implementation requires only minimal user input, while still being applicable to a range of *-seq protocols. We illustrate the advantages of a shape-based approach and describe the algorithmic principles underlying the implementation. In this paper, we present the ChIP-seq analysis tool available in CLC Genomics Workbench and CLC Genomics Server (version 7.5 and up), a user-friendly peak-caller designed to be not specific to a particular *-seq protocol. Current peak callers are often hard to parameterise and may therefore be difficult to use for non-bioinformaticians. Tested versions include OGE 6.2u6, PBS Pro11.0, LSF 8.3 and 9.1.Peak calling is a fundamental step in the analysis of data generated by ChIP-seq or similar techniques to acquire epigenetics information. CLC bio supports the third party scheduling systems OGE, PBS Pro, and IBM Platform LSF. CLC Server jobs can be sent from a master server out to grid nodes, where a grid scheduling system is used to handle job scheduling and submission. These serve as the core execution points of your bioinformatic services based on queue prioritization. Scalability With the built-in Job Node support of CLC Genomics Server, it is possible to attach an array of real or virtualized computers to the solution. The data management architecture offers very flexible built-in tools for restricting access and managing bioinformatics data. There are several approaches and options for customization such as plugin development and integration of external applications.įlexible data management CLC Genomics Server comes with a flexible data management solution for handling large amounts of genomics data. All connections from clients to the server are secured through SSL.Īdvanced customization CLC Genomics Server has been designed for advanced customization. This provides complete choice on the client-side of the system, including an option to design your own client. All are built on our service-oriented SOAP web-services. Multiple client options CLC Genomics Server comes with three client options: CLC Genomics Workbench, CLC Server Command Line Tools, and a web interface. ![]()
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