Peak Analysis
Useful peak manipulation (filter, comparison, and simulation) utilities.
| Tool Name | Input | Output | Description |
|---|---|---|---|
peak-align-ref | BED(ref) + BED(peak) | CDT | Align BED peaks to Reference BED file creating CDT files for heatmap generation. |
filter-bed | BED | BED(cluster) + BED(filter) | Filter BED file using user-specified exclusion zone using the score column to determine which peak to retain. |
tile-genome | genomeName | [BED|GFF] | Generate a coordinate file that tiles (non-overlapping) across an entire genome. |
rand-coord | genomeName | [BED|GFF] | Generate a coordinate file that tiles (non-overlapping) across an entire genome. |
sort-by-dist | BED/GFF | BED/GFF | Sort BED/GFF by distance to another BED/GFF (e.g. peak annotations). |
frix-score | BED + BAM | TXT | Quantify library enrichment around a set of Reference points (Fraction of Reads in Peak/Motif, aka FRiP/FRiM). |