Re: [Useq-users] R environment

[David N. <dav...@gm...>]

Could you send your command-line as well as a txt file containing a bit of
the input files (head input.txt > subInput.txt or gunzip ­c input.txt.gz |
head > subInput.txt if gzipped)?  I suspect the Tag2Point app is parsing on
white space and your number of columns is getting collapsed so that the
strand column is actually one less.

-cheers, David

From:  Radhouane Aniba <ar...@gm...>
Date:  Tue, 18 Oct 2011 10:41:55 -0400
To:  David Nix <dav...@gm...>
Cc:  <use...@li...>
Subject:  Re: [Useq-users] R environment

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