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  • VIB_user
    Junior Member
    • Oct 2010
    • 7

    Chip-seq analyse using USeq

    hi, i have a problem

    this is the first time i analyse Chip seq data and i have the following problem:

    i received my fastq data as txt files(not a problem) i converted this to sam and map files using bowtie this worked without any problem.
    now i want to go further with analysing this data using USeq,
    i followed the online tutorial file:///bioit/data/fasteris/USeq_7.0/Documentation/usage.html
    and it seemed to me that the Chipseq package is a good thing to start with to analyse it
    file:///bioit/data/fasteris/USeq_7.0/Documentation/cmdLnMenus.html#ChIPSeq

    so i have now .map and .sam files and my fastq files
    now they are talking about control alignment files and such, anyone know how to get these ?
    or someone that can explain but type of files each argument can be
    java -Xmx2G -jar pathTo/USeq/Apps/ChIPSeq -y eland -v D_rerio_Dec_2008 -t
    /Data/PolIIRep1/,/Data/PolIIRep2/ -c /Data/PolIINRep1/,/Data/PolIINRep2/ -s
    /Data/Results/WtVsNull -f /Anno/satelliteRepeats.bed

    tyvm

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