GenomeQuest CEO, Ron Ranauro, comments, “Our ChIP-Seq workflow is a great example of the power of SDM in the new era of next generation sequencing. Our goal is to provide researchers state-of-the-art, easy-to-use tools placed in a world-class, cloud computing infrastructure so they can focus on the expanding science, make great discoveries, and share their work – all from a web browser.” He continues, “And because our SDM is based on a web 2.0 open platform, researchers can be assured that GenomeQuest and our partners will enhance and add more and more NGS-enabled solutions at a compelling pace.”
The interactive sequence browser of the ChIP-Seq workflow includes a table of peak modeling results with columns for gene name and description, chromosome, peak start and stop position, peak length and high point, and all peak statistics. After their analysis, researchers can save all or part of this table as a new annotated database and share it as a reference for follow-on work.
Regarding parameters for ChIP-Seq methods, Nature Methods reports, “These parameters are often not fully known in advance, which means that computational analysis for a given experiment is usually performed iteratively and repeatedly, with results dictating whether additional sequencing is needed and is cost-effective. This means that the choice of software for running ChIP-Seq analysis favors packages that are simple to use repeatedly with multiple datasets.”
The GenomeQuest ChIP-Seq parameters for alignment include the read database, clean-up, low-quality base trimming and removal, and repeat removal. Peak modeling parameters for MACS include the aligned databa
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