---------- Forwarded message ---------- From: YOGESH OSTWAL firstname.lastname@example.org Date: Mon, Jul 11, 2011 at 1:34 PM Subject: Re: [galaxy-user] Hi To: Ido Tamir email@example.com
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 firstname.lastname@example.org 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.
- upload the data. (Get Data section)
- 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...