config.yaml

idx_bt1: /scratch/genomic_med/apps/annot/indexes/bowtie/hg19
macs_g: hs
macs_pvalue: 1e-5
macs2_g: hs
macs2_pvalue: 1e-5
macs2_pvalue_broad: 1e-5

control: 'Input'
#superEnhancer genome
rose_g: hg19

#number of reads downsample to, I set to 50 million, if reads number smaller than
## 50 million, downsample will keep the orignal reads
target_reads: 50000000

## run chromHMM or not
chromHMM: True

##chromHMM bin size
binsize: 200
#chromatin state model
state: 15
##chromHMM genome
chromHmm_g : hg19

## histone marks that you want to include in the chromHMM model
## space delimited. entries should be from the third column of the meta.txt file fed
## into the samples2json.py file.

histone_for_chromHMM: "K4me1 K4me3 K27ac K27me3"

# Path to a JSON file with samples and their corresponding FASTQ files.
SAMPLES: './SRR.txt'
SAMPLES_JSON: './samples.json'

CLUSTER_JSON: './cluster.json'