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!