Chip-seq analyse using USeq

[VIB_user]

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

[ETHANol]

"-c control alignment files directior" is your 'input' file to normalize against uneven genomic shearing and biases generated during library preparation.

For argument "-f Filter bed file" you need a bed file of repeats or whatever in the organism you are working in. Otherwise you can just leave it out.

You will not use your fastq files since they are not mapped.

Starting with ELAND files the ChIPSeq package doesn't work for me. I have to put the data through each file separately. Not a problem at all.