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.