Question: ChIP-seq. analysis Tutorial for Dummies
gravatar for chiefcat
23 months ago by
chiefcat100 wrote:

Hi all,

Does anyone know is there some material (e.g. books, webpage, etc.) really guides beginners for ChIP-seq. analysis?

I'm very struggling with the analysis since I don't have any background in handling NGS data or using command-line tools. However, I need to communicate with my labmates who use command-line tools (but without ChIP-seq analysis experience) for the analysis. Is there any detailed & practice materials for reading?

e.g. He did all the trimming, alignment, peak calling steps for me. When I want to use the output files for further analysis e.g. using deeptools, I really don't know if the output files we've got from his upstream works are suitable as the input of the next steps. Therefore, I want to understand the details (e.g. what kind of output files, details properties of those output files) of the tools he used but I found it hard to understand by just reading the website of the tools (e.g. Botie2, MACS2).

Do you guys have suggestion where should I start? Thanks a lot!


chip-seq dummy • 8.3k views
ADD COMMENTlink modified 22 months ago by Kevin Blighe46k • written 23 months ago by chiefcat100

You should additionally take a look at this thread, specifically focused on visualising ChIP-seq data: Visualization for ChIP-seq analysis

ADD REPLYlink written 22 months ago by Kevin Blighe46k
gravatar for Mike
23 months ago by
Mike1.3k wrote:

Have a look at following useful links...

ChIP-seq-analysis (one of the best link for beginners )

NGS data analysis with R / Bioconductor: ChIP-Seq workflow

Pipeline for ChIP-seq preprocessing

Analysis of ChIP-seq data

ENCODE TF ChIP pipeline using SPP and MACS2 for peak calling, and IDR for consistency analysis

ChIP-seq analysis

Hands-on introduction to ChIP-seq analysis - VIB Training

Practical Guidelines for the Comprehensive Analysis of ChIP-seq Data

ADD COMMENTlink written 23 months ago by Mike1.3k

Thanks Mike! I will read them. Tommy's page seems very informative and details. =]

ADD REPLYlink written 23 months ago by chiefcat100
gravatar for Gildas Le Corguillé
23 months ago by
France / Roscoff / ABiMS / Station Biologique de Roscoff
Gildas Le Corguillé20 wrote:

You can also have a look at what was done by the Galaxy Training Network (GTN) group :

ADD COMMENTlink written 23 months ago by Gildas Le Corguillé20
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