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cambiotraining / chipseq

ChIP-seq and ATAC-seq analysis
https://cambiotraining.github.io/chipseq/
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Datasets #11

Open tavareshugo opened 4 months ago

tavareshugo commented 4 months ago

This paper looks really nice: https://doi.org/10.1093/nar/gkad1225

Has ChIP-seq, ATAC-seq, RNA-seq, enough replicates, two groups (for differential binding).

SRA: https://www.ncbi.nlm.nih.gov/bioproject/?term=GSE196942

tavareshugo commented 2 days ago

Could use a separate dataset for demonstrating CUT&RUN.

This dataset has both ATAC-seq and CUT&RUN. It could be used as a kind of "capstone" exercise where they use the skills from the course to process these data. Might need some intro to specific software or considerations for CUT&RUN, but many of the concepts will overlap with ChIP-seq, so they can do the exercise by themselves.