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OpenOmics / chrom-seek

An awesome set of epigenetic pipelines for bulk cfChip-seq, ChIP-seq, and ATAC-seq
https://openomics.github.io/chrom-seek/
MIT License
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ATAC Conditional Rules #40

Closed schaughencyp closed 1 month ago

schaughencyp commented 5 months ago

For ATAC,

The following can be considered to probably be conditional when running the pipeline:

  1. Between macs2 and Genrich- Genrich should be default, macs2 should be conditional
  2. Between edgeR and deseq2 in the Diffbind rules - Deseq2 should be default, edgeR should be conditional.
  3. Motif analysis (MEME/Homer? rules) could probably be conditional for ATAC.
  4. Between genes, prot, protsec, protTSS - I think only prot needs to run by default. This should be a selection as the number of total jobs is ballooning in certain circumstances.

These are suggestions not demands,

Paul