Can you please recommend Chip-seq preprocessing tool

Question

[chansik]

Hi guys,

When I preprocess RNA-seq fastq files, I would use ngsShort, but it seems that people don't use ngsShort for Chip-seq quality control.

Can I ask you for recommendation of Chip-seq fsatq file preprocessing tool?

Thanks,

Answer 1

[ATpoint]

The easiest will be to just run it through the nf-core ChIP-seq pipeline:

https://github.com/nf-core/chipseq

Docs here:

https://nf-co.re/chipseq/1.2.1/usage

It is a fully-automated nextflow pipeline for alignment, peak calling and QC.

[chansik]

Thank yoy, ATpoint.

It seems very useful running the files with fully-automated pipeline.

But for me, as beginner, it is pretty hard to understand just reading docs. (I just finished installation, but don't know how to run it from creating a design file . and even my sample species, Cricetulus griceus is not listed in AWS iGenomes)

Are there on-line tutorial websites or videos available?

Thank you so much for your suggestion again!