Maybe with galaxy you don't have to program.
Its difficult to help you without knowing what your input data is.
If you have one IP file and one Input File from a TF binding
experiment from an Illumina machine
you have to:
0: have a look at the screencasts (galactic quickies) for some of the
1. upload the data. (Get Data section)
2. Do some quality statistics (FASTX-Toolkit for FASTQ data): Compute
Quality Statistics -> Draw ...
3. Map the input data files (NGS TOOLBOX BETA _ Map with Bowtie
4. call the peaks with e.g. MACS (also NGS toolbox).
5. visualize peaks and raw data in a genome browser (e.g UCSC, IGB or
then it gets more difficult with annotating the peaks etc...