SNEEP: SNP exploration and functional analysis using epigenetic data
- Getting started
- Examples of how to run SNEEP
- Optional input parameters
- Examples of realistic applications
- Example 1: Consider only TFs expressed in the cell type or tissue of interest
- Example 2: Consider only SNPs in the open chromatin of the cell type of interest
- Example 3: Associating regulatory SNPs with their target genes
- Example 4: Compute a proper random background control and highlight cell type-specific TFs
- Optional parameters
- Flag -o: Specify an output folder
- Flag -n: Number of threads
- Flag -p: p-value threshold for the TF binding score
- Flag -b and flag -x: base frequency for TF binding score computation
- Flag -c: p-value threshold for the absolute maximal differential TF binding score
- Flag -k: dbSNP database (dbSNPs_sorted.txt.gz)
- Flag -r and -g: Epigenetic interactions
- Flag -a: Store D:sub: max values for all considered shifts
- Flag -f: Include open chromatin data
- Flag -m: Get all D:sub: max values
- Flag -t, -d and -e: Active TFs of the cell type of interest
- Flag -j: Number of sampled background SNP sets
- Flag -l: Reproducible results for random background analysis
- Flag -q: TF count
- SNEEP result files
- References