DiffBind QC report

[tovahmarkowitz]

DiffBind QC report functionality needed for other assays beyond cfChIP

• make new subfolder in chrom-seek that creates a big csv file of all samples, one for each peak caller
• Also include in folder scripts and readme to make it easy for people to subset csv and run all steps automatically
• Incorporate https://github.com/OpenOmics/scribble/blob/main/scripts/ChIP_ATAC/DiffBind_PCA_normalizedCounts.R into functionality
• Think about adding actual html creation automatically for atac assay

[rroutsong]

@tovahmarkowitz what run modes do you want DiffBind_PCA_normalizedCounts.R to run under

and can you define specifically what you mean by scripts and readme you want to copy into your output directory

[tovahmarkowitz]

Okay, new plan. I completely forgot that the the DiffBindQC rule from the cfChIP assay should theoretically work on all our branches.

The Rmd (DiffBind_v2_cfChIP_QC.Rmd) should theoretically work under all conditions, BUT there are certain parameters that were set specifically for the PI who uses it the most.

So let's have two Rmds, one for cfChIP and one for everything else. I'll update the new one after you work out all the issues in getting it to run to completion.