FANTOMUS: Pipeline for clustering CAGE-seq bigWig files into promoters and enhancers using cagefightr

Files:

1. fantomus.r — main script that does clustering.
2. run_fantomus.sh — script we use to run the main script with default settings
3. paths.tsv — table containing paths to working dir, annotation files, etc.
4. release_name.txt — file containing current version name. By default this is the name of output folder

Inputs

1. "all" bigwig files. CTSS from CAGE-seq reads that do not necessary contain softclip at 5'-end.
2. "softclip" bigwig files. CTSS from CAGE-seq that contain softclip at 5'-end.
3. Annotation .gtf files: MANE and Gencode

Usage:

Simple:

bash run_fantomus.sh

Verbose:

Rscript fantomus.r -a <path to "all" bigwig folder>  -s <path to "softclip" bigwig folder> -o <path to output folder>

Resources

1. cagefightr
2. Combat-ref