Chip-seq analyse using USeq

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Join Date: Oct 2010

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Chip-seq analyse using USeq

10-04-2010, 06:17 AM

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
Tags: chip seq, chip-seq analysis, chipseq, fastq fasta reads, useq

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