Repository of scripts that I've made/appropriated and general tidbits. Obviously varies case by case, but core steps are described in:

• MNase-seq Standard Processing Pipeline (using danpos)
• MNase-seq Processing Pipeline using totalcoverage approach
• RNA-seq Processing Pipeline
• Metagenomics Processing Pipeline
• SLURM compute cluster
• Miscellaneous steps and tidbits

Otherwise jump into the scripts folders of:

• Core scripts: Things that are completed and have posix or flag based input

• BAM2SizePlot.py is the package for 3D plotting size differentiateing chromatin accessibility data.

• R-scripts: Often esoteric and environment-specific processing and charting mid-length scripts, ask if explanation needed.

• General Tidbits: Helpful oneliners and notes

• Unfinished: Scripts that are still in progress, or have been paused for a later date. Would not recommend.