git clone https://github.com/jsh58/Genrich
cd Genrich
make

conda install macs2

ssh bio1
## start a screen session
screen
git clone https://github.com/crazyhottommy/Genrich_compare
## make samples.json file
python sample2json.py /path/to/fastq/dir meta.txt

cat meta.txt
sample fastq factor read
SRR891269 SRR891269_GSM1155958_GM12878_ATACseq_50k_Rep2_Homo_sapiens_OTHER_1.fastq.gz atac R1
SRR891269 SRR891269_GSM1155958_GM12878_ATACseq_50k_Rep2_Homo_sapiens_OTHER_2.fastq.gz atac R2
SRR891270 SRR891270_GSM1155959_GM12878_ATACseq_50k_Rep3_Homo_sapiens_OTHER_1.fastq.gz atac R1
SRR891270 SRR891270_GSM1155959_GM12878_ATACseq_50k_Rep3_Homo_sapiens_OTHER_2.fastq.gz atac R2
SRR891271 SRR891271_GSM1155960_GM12878_ATACseq_50k_Rep4_Homo_sapiens_OTHER_1.fastq.gz atac R1
SRR891271 SRR891271_GSM1155960_GM12878_ATACseq_50k_Rep4_Homo_sapiens_OTHER_2.fastq.gz atac R2
SRR891272 SRR891272_GSM1155961_GM12878_ATACseq_500_Rep1_Homo_sapiens_OTHER_1.fastq.gz atac R1
SRR891272 SRR891272_GSM1155961_GM12878_ATACseq_500_Rep1_Homo_sapiens_OTHER_2.fastq.gz atac R2
SRR891273 SRR891273_GSM1155962_GM12878_ATACseq_500_Rep2_Homo_sapiens_OTHER_1.fastq.gz atac R1
SRR891273 SRR891273_GSM1155962_GM12878_ATACseq_500_Rep2_Homo_sapiens_OTHER_2.fastq.gz atac R2
SRR891274 SRR891274_GSM1155963_GM12878_ATACseq_500_Rep3_Homo_sapiens_OTHER_1.fastq.gz atac R1
SRR891274 SRR891274_GSM1155963_GM12878_ATACseq_500_Rep3_Homo_sapiens_OTHER_2.fastq.gz atac R2

sample fastq_name factor reads
C57BL SRR534669.fastq.gz Per2 R1
C57BL SRR534670.fastq.gz Per2 R1
C57BL SRR534671.fastq.gz Per2 R1
C57BL SRR534672.fastq.gz Per2 R1
C57BL SRR534673.fastq.gz Per2 R1
C57BL SRR534674.fastq.gz Per2 R1
C57BL SRR534676.fastq.gz Input R1

sample fastq_name factor reads
LKR10 Input_LKR10_1.fq.gz Input R1
LKR10 Input_LKR10_2.fq.gz Input R2
V6_5 Input_V6_5_1.fq.gz Input R1
V6_5 Input_V6_5_2.fq.gz Input R2
LKR10 Mll4_LKR10_1.fq.gz Mll4 R1
LKR10 Mll4_LKR10_2.fq.gz Mll4 R2
LKR10 Per2_A_LKR10_1.fq.gz Per2A R1
LKR10 Per2_A_LKR10_2.fq.gz Per2A R2
LKR10 Per2_B_LKR10_1.fq.gz Per2B R1
LKR10 Per2_B_LKR10_2.fq.gz Per2B R2
V6_5 Per2_B_V6_5_1.fq.gz Per2 R1
V6_5 Per2_B_V6_5_2.fq.gz Per2 R2

## whether it is from fastq files or from bam files
from_fastq: True
## the reads are paired end or single end
paired_end: True
# >70bp long, <70bp false
long_reads: True
# what's the control for IP
# if it is ChIP-seq data
# this is the same as the third colmn of the meta.txt factor column
control: 'Input'
## if it is ChIP-seq data without Input/IgG control or ATACseq data (without control by nature)
## set control : False
## the reference fasta path
ref_fa: "/n/regal/informatics_public/reference_genome_by_tommy/ucsc/mm9/mm9.fa"
macs2_g: mm
macs2_pvalue: 1e-5
# other macs2 arguments
macs2_args: -f BAM
Genrich_args: "-r -p 0.05 -a 200 "
#number of reads downsample to, I set to 50 million, if reads number smaller than
## 50 million, downsample will keep the orignal reads.
## if downsample set to False, no downsample will be done, symbolic link will be used
downsample: False
target_reads: 50000000

## set up the config.yaml file
nano config.yaml
## dry run
snakemake -np
## real run
snakemake -j 24
## submit to slurm
./pyflow_Genrich_compare.sh