On Jul 10, 2011, at 8:00 AM, YOGESH OSTWAL wrote:

> Dear Galaxy users,
> This is Yogesh, a new galaxy user, very new to programming as well. Can 
> anybody guide me from where to start to learn ChIP-Seq analysis?
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 tasks.
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...

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