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epigen / atacseq_pipeline

Ultimate ATAC-seq Data Processing, Quantification and Annotation Snakemake Workflow and MrBiomics Module.
https://epigen.github.io/atacseq_pipeline/
MIT License
47 stars 2 forks source link

Compatibility outside ATAC-seq data #50

Closed BiotechPedro closed 2 months ago

BiotechPedro commented 2 months ago

Hi :D

Since I really like this pipeline, I was wondering which one do you use to process ChIP-seq (or ChIPmentation) data. Is it this one or do you use another one?

Many thanks!

peter

sreichl commented 2 months ago

Hi Peter, thanks for reaching our and your kind words. Currently, we do not have any projects with ChIP-seq data, and we haven't had in a while. Therefore we do not offer a dedicated workflow for the processing/analysis of ChIP-seq data. As far as I know the raw data is very similar to ATAC-seq so feel free to check the specific steps of this workflow and/or try to proceess your data with it. I would be curious about your experience.

For downstream analysis or other modalities I would like to refer your to the project's main repository: MR.PARETO.

Please feel invited to star and share modules you find valuable. This help others discover them, and guides our future work!

Thanks & Cheers, Stephan