GenomeQuest Places ChIP-Seq Workflow Solution on SDM “Cloud”
Product News Nov 13, 2009
GenomeQuest has announced a comprehensive and easy-to-use ChIP-Seq workflow solution available immediately as a web cloud service to researchers around the world.
The ChIP-Seq method is described in this month’s Nature Methods journal, “Genome-wide measurements of protein-DNA interactions and transcriptomes are increasingly done by deep DNA sequencing methods (ChIP-Seq and RNA-Seq).”
Reporting on tools, it continues, “Whereas early adopters necessarily developed their own custom computer code to analyze the first ChIP-Seq and RNA-Seq datasets, a new generation of more sophisticated algorithms and software tools are emerging to assist in the analysis phase of these projects.”
Based on the company’s SDM platform and integrating the popular Model based Analysis for Chip-Seq “MACS” peak modeling software, the GenomeQuest ChIP-Seq solution provides state-of-the-art tools across the entire workflow, including for alignment, peak modeling, and interactive analysis.
To maximize accuracy, it allows for over 15 key parameters to be set and multiple runs to be stacked and analyzed collectively. Also, researchers can immediately share and connect their results with other sequence databases, GenomeQuest workflows, and colleagues – preserving and leveraging their work.
This full workflow is delivered in an easy-to-use, integrated environment. From a web browser, researchers simply upload their database and fill out two forms – one each for alignment and peak modeling. For the reference databases, users can select from a list of GenomeQuest aggregated and qualified databases with extended annotations. The environment also includes an interactive sequence browser where researchers query and analyze run results.
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 database, control alignment database (optional), mappable genome size, sequence read size, and sheared genomic fragment size.
Commenting on the investigative power of a series of workflows in a discovery progression, GenomeQuest Field Application Scientist Henk Heus Senior Director of Workflow Development offers, “In GenomeQuest, you can combine the outcome of different workflows directly within the web interface. Think about being able to find gene regulatory regions using the ChIP-Seq workflow, finding SNPs in those regulatory regions using the Variant workflow and then see if these SNPs change gene expression levels using the RNA-Seq workflow. This is all possible without writing a single line of code.”
Researchers can use the ChIP-Seq and all GenomeQuest workflows at no charge on sample or real projects by registering for a free Basic Account. The free Basic Account gives researchers access to all ChIP-Seq and SDM functionality, complete results of Sanger sequence runs, and a sampling of NGS run results. There is no obligation, no credit card required, and no software to install. The site includes online help/chat and sample sequence databases.
Registrants for ChIP-Seq can also apply for a free Silver Account, which gives access to all results of NGS runs and is generally available for annual subscription starting at $1500 (US). This limited time offer is available to the first 100 qualified applicants.
A video preview of the GenomeQuest ChIP-Seq workflow is available, and more detailed information is available at the GenomeQuest product wiki. The full Nature Methods article on ChIP-Seq is available on its online site.
Full details of the open source MACS technology and bios of authors Yong Zhang and Tao Liu are available on its product website and in their paper, published in Genome Biology.