---------- Forwarded message ----------
From: YOGESH OSTWAL <yogeshfreeb...@gmail.com>
Date: Mon, Jul 11, 2011 at 1:34 PM
Subject: Re: [galaxy-user] Hi
To: Ido Tamir <ta...@imp.ac.at>

thanks a lot.

Sorry for disturbing you again.

Before starting with the actual data, can I try this analysis with already
available IP and input files of datasets of illumina from NGS repository?

On Mon, Jul 11, 2011 at 12:29 PM, Ido Tamir <ta...@imp.ac.at> wrote:

> 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
> trackster).
> then it gets more difficult with annotating the peaks etc...
> best,
> ido

Regards -


Regards -

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