
Hello Joern,

 

I am having some trouble with the mapping of the reporters to the genomic positions.

 

1. I have downloaded the ccTutorial and have takena look at the exonerateData folder. I was wondering how I could create a .fsa file like RenMM5TilingProbe-Sequences.fsa from my Nimlegen .ndf file for the sequences for all the reporters on my 385k chip?

 
2. I have the .sh and .pl files in the exonerateData folder. Once I have my .fsa file from above, what exactly do I need to run to create the "allChromExonerateOut.txt" file?Do all the files ...   .fsa, .sh and the .pl have to be in the current working directory?
 
 
 Thanks in advance!
 
Best Regards,
Som.
 

 


 
> From: Joern.Toedling@curie.fr
> To: bioconductor@stat.math.ethz.ch
> Date: Sat, 6 Mar 2010 09:58:21 +0100
> Subject: Re: [BioC] chip-chip data
> 
> Hi Som,
> 
> there also is a Plos Computional Biology article, which also provides many
> details on how to use Ringo:
> http://tinyurl.com/ydvrjq8
> You may also want to have a look at the associated data package "ccTutorial".
> 
> Best regards,
> Joern
> 
> On Fri, 5 Mar 2010 11:42:30 -0800, Noah Dowell wrote
> > The vignettes for Starr and Ringo are quite helpful for getting 
> > started on reading in your files, processing and normalization. 
> > There is also a publication associated with Ringo for a little more 
> > explanation. It seems like you have all of the files so just fire 
> > up Ringo and see how it works :). (There are example data "made" for 
> > Ringo that you can use to test it out and make sure your files look 
> > like they "should.")
> > 
> > Here is the link to the vignette:
> > 
> > Ringo:
> > 
> >
> http://www.bioconductor.org/packages/release/bioc/vignettes/Ringo/inst/doc/Ringo.pdf
> > 
> > And the paper citation:
> > 
> > J. Toedling, O. Sklyar, T. Krueger, J. J. Fischer, S. Sperling, and 
> > W. Huber. Ringo - an R/Bioconductor package for analyzing ChIP-chip 
> > readouts. BMC Bioinformatics, 8:221, 2007.
> > 
> > I am certainly not the expert on this board but if you start to get 
> > specific errors (on your data analysis) after you read through the 
> > vignette and worked with the example data then post them and I will 
> > do my best to help out.
> > 
> > noah
> > 
> > Hello Noah,
> > 
> > Thanks for the suggestions. Do you have a protocol or something for 
> > Starr or Ringo? I am starting from .pair, .ndf, .pos and .gff (for 
> > the nimblegen refseq mouse genome) nimblegen files. I would really 
> > appreciate it if you would share your protocol/s.
> > 
> > Thanks so much,
> > Som.
> > 
> 
> ---
> Joern Toedling
> Institut Curie -- U900
> 26 rue d'Ulm, 75005 Paris, FRANCE
> Tel. +33 (0)156246927
> 
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