ATACprofWS.conf

# Modify path in this file
$ATACprofWS_ROOT = "/home/park/Miyanari/ATAC/ATACprofWS/";

# TOOLs
$BTB    = "/home/park/TOOL/BEDTools/bin/bamToBed";
$INTB   = "/home/park/TOOL/BEDTools/bin/intersectBed";
$MERGEB = "/home/park/TOOL/BEDTools/bin/mergeBed";
$COVB   = "/home/park/TOOL/BEDTools/bin/coverageBed";
$MACS2  = "/home/park/.local/bin/macs2";

# Directories
$ANNOT_DIR = $ATACprofWS_ROOT . "data/";

### windows bin = 10K
$SL_WIN = "10K";
$GL_10K = $ANNOT_DIR . "Genome_Bed/hg38_10k.bed";
$BLACK_LIST = $ANNOT_DIR . "Blacklist/hg38.chipseq.chrM.combined.bed";

# Which is the Control Sample ID?
$CTRL = "NC";

# Parameters
$BW_BIN     = 50; # bigwig bin size 
$DENOVO_CUT = 1;  # if <1 scaled read count, the value set to zero
$DENOVO_CUT_GENE = 10; # cutoff for clustering
$MIN_SCALED_READ_CUT = 10;

$PVAL_THRESH = 0.01; #for MACS2 pvalue threshold
$SMOOTH_WIN  = 150;  #for MACS2 smoothing window
$SHIFT_SIZE  = int( $SMOOTH_WIN / 2.0) * -1; #for MACS2 shift (-1* half_size of ext)

$FDR_THRES = 0.01; # for capturing peak positions (uniq, denovo)
## MACS2 option
$MACS2_OPT   = "callpeak --nomodel --shift " . $SHIFT_SIZE . " --extsize " . $SMOOTH_WIN . " -g hs -p " . $PVAL_THRESH . " -B --SPMR --keep-dup all --call-summits -f BED";
# B: pileup, local lambda
# SPMR: signal per millioin reads


1;