
Hello Joern,

 

Thanks for all the suggestions. In my experiment, I had 3 replicates for WT and 3 replicates for knockouts and each had respective inputs. Could you please suggest me a way to use the replicate information? The examples you had dinot have replicates in them. Any suggestions would be greatly appreciated.
Thanks,

Som.

 
> From: Joern.Toedling@curie.fr
> To: bioconductor@stat.math.ethz.ch; genome1976@hotmail.com
> Subject: RE: [BioC] chip-chip data
> Date: Mon, 8 Mar 2010 10:42:31 +0100
> 
> Hi Som,
> 
> On Sun, 7 Mar 2010 15:56:15 -0500, somnath bandyopadhyay wrote 
> > Hello Joern, 
> >   
> > I am having some trouble with the mapping of the reporters to the genomic
> positions. 
> 
> there are many ways to map the reporter sequences to the genome and the one
> using Exonerate that is mentioned in the tutorial is just one of them, so you
> could use an alternative one that you are more familiar with.
> For example, using the Biostrings function "matchPDict", you can even do this
> in R now.
> 
> >   
> > 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? 
> 
> These sequences are one of the columns of the ndf file (the sixth, I think).
> Also unique identifiers for each reporter are given in another column of that
> file. So you need to extract these two columns and write them out into a
> Fasta-file. You can read in the file into R using "read.delim" and then use
> the function "cat" to export just two of the columns.
> The package Ringo also contains a Perl script "extractProbeSequenceFasta.pl"
> in its scripts directory which performs the same task.
> 
> >   
> > 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? 
> 
> Basically, you need to modify the .sh file to change the paths such that the
> work for you system. The Perl script in there is just for combining the
> multiple output files from Exonerate into one file.
> 
> For details on the Exonerate parameters, please read the manual that comes
> with Exonerate. And again, if you are not happy with Exonerate, you also use
> another tool for this step.
> 
> Regards,
> Joern
> 
> 
> --- 
> Joern Toedling 
> Institut Curie -- U900 
> 26 rue d'Ulm, 75005 Paris, FRANCE 
> Tel. +33 (0)156246927
> 
 		 	   		  
_________________________________________________________________
Hotmail: Free, trusted and rich email service.

	[[alternative HTML version deleted]]

