config.yaml

# Blacklist file of common false-positive sites in the genome
# Downloaded from https://sites.google.com/site/anshulkundaje/projects/blacklists
blacklist: "/gpfs/home/mjohnston/reference/hg38.blacklist.bed.gz"

# Broad peak calls. Separate threshold for broad peaks.
# Will be interpreted as q-value due to -q specified for q_val
broad_cutoff: "0.1"

# Genome chromosome sizes needed for IGV-viewable TDF
chrom_sizes: "/gpfs/gallo/michael/reference/hg38.chrom.sizes"

# Effective genome size required by DeepTools normalization to RPGC - reads per genomic content
# Homo sapiens 2750000000 taken from https://www.nature.com/articles/nbt.1518/tables/1  @70bp seq length
eff_genome: "2750000000"

# Specify genome to align against and system path
genome_path: "/gpfs/gallo/michael/reference/hg38.fa"

# Genome size argument for MACS
# hs for homo sapiens
genome_size: "hs"

# ChIP sample names. List of lists of pairs. [ip_name, input_contol_name]
# Assumes fastq file names end with .R1.fastq
ip_input_pairs: [["samp1_ip.rep1", "samp1_input"],["samp1_ip.rep2", "samp1_input"],["samp2_ip.rep1", "samp2_input"],["samp2_ip.rep2", "samp2_input"]]

# Minimum alignment quality threshold for samtools alignment filtering
min_aln_q: 30

# q-value for MACS peak calls.
# In broad peakcalling mode, MACS2 uses -q or -p setting to define regions within broadpeaks as 'stronger' enrichment.
q_val: 0.05

# Location for temporary files to be written
tmp_dir: "/home/mjohnston/tmp"