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Old 08-01-2008, 05:45 AM   #1
kmay
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Default Genomatix offerings

Quote:
Originally Posted by Inti View Post
Does any of you guys have tryed the Genomatix products for Next Gen Seq?
Hi!

Since Inti asked and no one replied, may I jump in here.
I am from Genomatix and may have a rather biased view

With the increasing data load from NGS, we decided to move from web based services to delivering turnkey systems on site.
Currently there are two offerings:

ATTENTION commercial advertizing following:
Genomatix delivers powerful turnkey solutions downstream of Next Generation Sequencing (NGS) devices, following the Genomatix tradition of highest scientific standards and cutting edge technology.
Genomatix solutions work with data from all available NGS system providers: Illumina´s Genome Analyzer (Solexa), Roche (454), The SOLiD TM System by Applied Biosystems, and HeliScope by Helicos.

Genomatix Mapping Station (GMS) delivers ultra-fast mapping of sequence reads of any length above 9 base pairs. Ten million typical NGS reads of variable lengths are perfectly and uniquely mapped to the human genome in less than 30 minutes. GMS is flexible and allows for any number of indels and point mutations, delivering an uniqueness measure for each mapped read. It takes the NGS system internal error checking into account and detects new SNPs. Cutting edge technology identifies splice junction tags for advanced transcriptome analysis.

Genomatix Genome Analyzer (GGA) is the complete solution for ChIP-seq and transcriptome analysis downstream of mapping the NGS system reads to the genome with the Genomatix Mapping Station, or any other technology. Terabytes of annotation data complement the results from the NGS experiment and expand by optional integration with each new sequencing run to a customized genome database. Easy-to-use visualization and genome wide correlations allow for meta-analysis of all kind of data-sets.
Integrated comparative genomics procedures allow for phylogenetical conservation analysis of findings.
Genome wide transcription factor analysis, gene regulatory region analysis, regulatory SNPs, epigenetic modification analysis, DNase-seq, digital gene expression with normalization and quantification of expression values… all required data and hardware in one technology unit at your lab. GGA is operated through a comprehensive easy-to-use web based interface for the biologist, plus features full data structure access and command line driven procedures for the bio-informatician for easy integration into own high-throughput pipelines
End of commercial advertizing

The above would fit to integrated solutions.

The following solutions are web-based and free for everybody up to two weeks after signing up for a test account.

ChIP-Seq. RegionMiner

Genome Annotation/Genome Browser: ElDorado

Personal annotation up to 10 times 10 million regions can be uploaded into ElDorado through RegionMiner.

Then, Genomatix offers analysis services

Example data for Boyle´s Solexa DNase-seq data is here

(lower picture is clickable)

Sorry, if this posting is too commercial. I promise, I won´t do it again

Klaus
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Old 08-01-2008, 08:47 AM   #2
ECO
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No worries Klaus! I just moved it to it's own thread to make it easier to find.

Plus I'm interested in a beta/trial...so I'll be contacting you!
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Old 08-01-2008, 10:52 AM   #3
Nix
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Default Algorithms?

Hello Klaus,

Have you published or described anywhere the statistical basis and performance of your RegionMiner chIP-seq detector?
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Old 08-01-2008, 12:49 PM   #4
kmay
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Originally Posted by Nix View Post
Hello Klaus,

Have you published or described anywhere the statistical basis and performance of your RegionMiner chIP-seq detector?
Hi Nix!

What are you referring to? The mapping procedures and how to detect tag-enrichment? We call this tag-clustering.
This is not published, yet but no big deal. We work with a sliding window approach and base the statistics on a poisson distribution. Depending on the type of experiment ( ChIP-seq, RNA-seq, DGE etc) different parameters, like genome, promoter counts and lengths, exon counts and legths go into statistics to calculate the probability to find a cluster at given probability by chance.
But i am not expert in this. I´ll ask my colleague who developed the stuff to join the board and give exact answer.

RegionMiner starts after clustering, when you have your significantly enriched regions defined. It is a collection of several tools.Here different statistical approaches are applied. Best if you read through the online help pages

All our peer reviewed papers about Methods are here
Not all of them apply to RegionMiner, but certainly those about MatInspector ( when you are IP-ing TFs).

Then when it comes to promoter analysis our scientific FAQ might be helpful.

Cheers

Klaus
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