---------- 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 - Yogesh -- Regards - Yogesh
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