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gravatar for YOGESH OSTWAL
7.4 years ago by
YOGESH OSTWAL • 20
YOGESH OSTWAL • 20 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? -- Regards - Yogesh
chip-seq • 736 views
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modified 7.4 years ago by Ido M. Tamir • 280 • written 7.4 years ago by YOGESH OSTWAL • 20
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gravatar for Ido M. Tamir
7.4 years ago by
Ido M. Tamir • 280
Austria
Ido M. Tamir • 280 wrote:
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
ADD COMMENT • link written 7.4 years ago by Ido M. Tamir • 280
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gravatar for Ido M. Tamir
7.4 years ago by
Ido M. Tamir • 280
Austria
Ido M. Tamir • 280 wrote:
why shouldn't you? select something from geo or from a paper. http://www.ncbi.nlm.nih.gov/geo/ Use a download manager to download the big files. best, ido
ADD COMMENT • link written 7.4 years ago by Ido M. Tamir • 280
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