ChIP-seq analysis: Tutorial for Beginners

Question

[chiefcat]

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!

Kylie

[Kevin Blighe]

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

Answer 1

[Mike]

Have a look at following useful links...

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

https://github.com/crazyhottommy/ChIP-seq-analysis

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

http://biocluster.ucr.edu/~rkaundal/workshops/R_feb2016/ChIPseq/ChIPseq.html

Pipeline for ChIP-seq preprocessing

https://github.com/shenlab-sinai/chip-seq_preprocess

Analysis of ChIP-seq data

https://galaxyproject.org/tutorials/chip/

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

https://github.com/mforde84/ENCODE_TF_ChIP_pipeline

ChIP-seq analysis

https://www.ebi.ac.uk/training/online/course/ebi-next-generation-sequencing-practical-course/gene-regulation/chip-seq-analysis

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

http://www.biologie.ens.fr/~mthomas/other/chip-seq-training/

Practical Guidelines for the Comprehensive Analysis of ChIP-seq Data

http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003326

[chiefcat]

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

Answer 2

[Gildas Le Corguillé]

You can also have a look at what was done by the Galaxy Training Network (GTN) group : http://galaxyproject.github.io/training-material/topics/chip-seq/