Re: [Useq-users] R environment

[Radhouane A. <ar...@gm...>]

Thank you David,

It works but generated a bug I dont understand it, sorry I am just starting
using it :

Parsing PointData from raw alignments...
    Parsing treatment PointData...
    /fs/sh-data/USeq/Data/DNAse/RESULTS/PointData/TreatmentPointData/Rep0
java.lang.ArrayIndexOutOfBoundsException: 5
    at
edu.utah.seq.parsers.Tag2Point.splitBedFilesToTemp(Tag2Point.java:206)
    at edu.utah.seq.parsers.Tag2Point.<init>(Tag2Point.java:76)
    at edu.utah.seq.analysis.ChIPSeq.parsePointData(ChIPSeq.java:306)
    at edu.utah.seq.analysis.ChIPSeq.parsePointData(ChIPSeq.java:236)
    at edu.utah.seq.analysis.ChIPSeq.<init>(ChIPSeq.java:73)
    at edu.utah.seq.analysis.ChIPSeq.main(ChIPSeq.java:449)

My Input files are in this format :

chr1    161    181        250    +
chr1    164    184        250    +
chr1    237    257        333    +

Thanks

Radhouane



2011/10/18 Radhouane Aniba <ar...@gm...>

> I am using the Chip-seq app will take a look at its options.
>
> Radhouane
>
>
> 2011/10/18 David Nix <dav...@gm...>
>
>> Hello Radhouane,
>>
>> I believe each of the apps that use R have a –r option that lets you
>> specify where R is?  Which app were you trying to run? Did you take a look
>> at the command line options (launch the app with no arguments).  -cheers, D
>>
>>
>>
>> From: Radhouane Aniba <ar...@gm...>
>> Date: Tue, 18 Oct 2011 10:18:06 -0400
>> To: <use...@li...>
>> Subject: [Useq-users] R environment
>>
>> Hello everyone,
>>
>> Is there any option with USeq where we can specify the location of R
>> binaries, I am working on a server on which I have no permission to change
>> R, so I installed R-2.13.0 in a different folder made my setenv changes but
>> I have an error message saying :
>>
>> Cannot find or execute the R application -> /usr/bin/R
>>
>> Any help ?
>>
>> Thanks
>>
>> Radhouane
>>
>>
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>
>
>
> --
> *Radhouane Aniba*
> *Bioinformatics Postdoctoral Research Scientist*
> *Institute for Advanced Computer Studies
> Center for Bioinformatics and Computational Biology* *(CBCB)*
> *University of Maryland, College Park
> MD 20742*
>
>


-- 
*Radhouane Aniba*
*Bioinformatics Postdoctoral Research Scientist*
*Institute for Advanced Computer Studies
Center for Bioinformatics and Computational Biology* *(CBCB)*
*University of Maryland, College Park
MD 20742*