3. DROMPAplus: read distritbution

drompa+ can visualize multiple ChIP samples with specified genome annotation, using modes for the implementation of various types of ChIP-seq analysis:

• PC_SHARP: peak-calling (for sharp mode)

• PC_BROAD: peak-calling (for broad mode)

• PC_ENRICH: peak-calling (enrichment ratio)

• GV: global-view visualization

• PROFILE: makes a PDF file and corresponding R script of the averaged read density (also used to make a PNG file and corresponding Python script)

• MULTICI: generate matrix of averaged read density

• GENWIG: generates wig data of ChIP/Input enrichment and p-value distributions

Note that the algorithms for PC_SHARP, PC_BROAD and PC_ENRICH are identical. Only the default parameter sets differ. A sample script file can be found in the “tutorial” directory. sample.human.sh describes the tutorial of these commands of drompa+ for the histone modification data of human K562 cells.

• 3.1. PC_SHARP: Read distribution visualization
• 3.2. PC_ENRICH: Enrichment visualization
• 3.3. Peak-calling
• 3.4. GV: chromosome-wide overview
• 3.5. PROFILE: Aggregation plot (using R)
• 3.6. HEATMAP (using Python3)
• 3.7. MULTICI: Generate matrix of averaged read density
• 3.8. GENWIG: Generate wig data