Bacon

	step1: Linker trimming	step2: Read alignment & PET filtering	step3: call peaks & count loops	step4: Estimate significance
ChIA-PET2	√	√	√	√
mango	√	√	√	√
ChIA-PETv3	√	√	√	√
ChIAPoP	√	√	√	√
CID	-	-	√	√
cLoops	-	-	√	√
ChiaSig	-	-	-	√

ChIA-PET2

Li G, Chen Y, Snyder MP, Zhang MQ. 2017. ChIA-PET2: a versatile and flexible pipeline for ChIA-PET data analysis. Nucleic Acids Res 45: e4–e4.

Command line

ChIA-PET2 -g /bwa_index/mm10.fasta -b /ChIA-PET2/example/mm10.chrom.sizes -f /mES-SMC_raw/SRR1296617_1.fastq.gz -r /mES-SMC_raw/SRR1296617_2.fastq.gz -A CTGCTGTCCG -B CTGCTGTCAT -o /mES-SMC_out/CP2_rep1 -n mes_mis0 -e 0 -m 0 -d 1 –t 6

ChIA-PET2 -g /bwa_index/mm10.fasta -b /ChIA-PET2/example/mm10.chrom.sizes -f /k562-H3k27ac_raw/SRR1514661_1.fastq.gz -r /k562-H3k27ac_raw/SRR1514661_2.fastq.gz -A GTTGGATAAG -B GTTGGAATGT -o /k562-H3k27ac_out/CP2_rep1 -n h3_mis1 –e 1 -m 0 -d 1 -t 6

mango

Phanstiel DH, Boyle AP, Heidari N, Snyder MP. 2015. Mango: a bias-correcting ChIA-PET analysis pipeline. Bioinformatics 31: 3092–3098.

Command line

Rscript mango.R --fastq1 /mES-SMC_raw/SRR1296617_1.fastq --fastq2 /mES-SMC_raw/SRR1296617_2.fastq --prefix mES --outdir /mango/mES_rep1 --linkerA CTGCTGTCCG --linkerB CTGCTGTCAT --argsfile /mango/argfile.txt --stages 1:5 --maxlength 100 --gsize mm

Rscript mango.R --fastq1 /k562-H3k27ac_raw/SRR1514661_1.fastq --fastq2 /k562-H3k27ac_raw/SRR1514661_2.fastq --prefix k562_h3 --outdir /mango/mango_rep1/ --linkerA GTTGGATAAG --linkerB GTTGGAATGT --maxlength 100 --argsfile /mango/argsfile.txt --stages 1:5 --gsize hs --biascut 0.5

ChIA-PETv3

Li G, Sun T, Chang H, Cai L, Hong P, Zhou Q. 2019. Chromatin Interaction Analysis with Updated ChIA-PET Tool (V3). Genes-basel 10: 554.

Command line

java -jar /ChIA-PET_Tool_V3/ChIA-PET.jar --mode 0 --fastq1 /mES-SMC_raw/SRR1296617_1.fastq --fastq2 /mES-SMC_raw/SRR1296617_2.fastq --linker /ChIA-PET_Tool_V3/linker/linker_mES.txt --minimum_linker_alignment_score 5 --GENOME_INDEX /bwa_mm10/mm10.fasta --GENOME_LENGTH 1.87e9 --CHROM_SIZE_INFO /ChIA-PET_Tool_V3/chromInfo/mm10.chrom.sizes.txt --CYTOBAND_DATA /ChIA-PET_Tool_V3/chromInfo/mm10_cytoBandIdeo.txt --SPECIES 2 --output /CPT3_rep1 --prefix mES --thread 4 --minimum_tag_length 15 --minSecondBestScoreDiff 1

java -jar /ChIA-PET_Tool_V3/ChIA-PET.jar --mode 1 --fastq1 /k562-H3k27ac_raw/SRR1514661_1.fastq --fastq2 /k562-H3k27ac_raw/SRR1514661_2.fastq --linker /ChIA-PET_Tool_V3/linker/linker_long.txt --minimum_linker_alignment_score 8 --GENOME_INDEX /bwa_hg19/hg19.fa --GENOME_LENGTH 3E9 --CHROM_SIZE_INFO /ChIA-PET_Tool_V3/chromInfo/hg19.chromSize.txt --CYTOBAND_DATA /ChIA-PET_Tool_V3/chromInfo/hg19_cytoBandIdeo.txt --SPECIES 1 --output ./CPTV3 --prefix h3k27ac_rep1 --thread 4 --minimum_tag_length 15 --minSecondBestScoreDiff 1

ChIAPoP

Huang W, Medvedovic M, Zhang J, Niu L. 2019. ChIAPoP: a new tool for ChIA-PET data analysis. Nucleic Acids Res 47: gkz062-.

Command line

trim.linkers("/mES-SMC_raw/SRR1296617_1.fastq.gz","/mES-SMC_raw/SRR1296617_2.fastq.gz", linkers = c("CTGCTGTCCG"," CTGCTGTCAT"), destination.regular = c("regular_m0_1.fastq","regular_m0_2.fastq"), destination.chimeric = c("chimeric_m0_1.fastq","chimeric_m0_2.fastq"),mh=0) fqlist<-c("regular_m0_1.fastq","regular_m0_2.fastq","chimeric_m0_1.fastq","chimeric_m0_2.fastq") align_reads(fqlist, bowtieidex, bowtieCMD)
process.sam("regular_m0_1.sam","regular_m0_2.sam",PET.strand.info = TRUE, remove.old.sam = TRUE)
process.sam("chimeric_m0_1.sam","chimeric_m0_2.sam",PET.strand.info = FALSE)
call.peaks("macs2", c("regular_m0_1_processed.sam", "regular_m0_2_processed.sam","chimeric_m0_1_processed.sam", "chimeric_m0_2_processed.sam"), gsize = "mm", chr.include = "all")
count.interactions("regular_m0_1_processed.sam", "regular_m0_2_processed.sam", "chimeric_m0_1_processed.sam", "chimeric_m0_2_processed.sam","macs2_peaks.narrowPeak", "regular_count.txt", "chimeric_count.txt", "anchor_info.txt", distance.strand.file = "PET_distance_strand.txt", ref.genome ="mm10")
pop.test("regular_count.txt", "chimeric_count.txt", "anchor_info.txt", "result.txt", ref.genome = "mm10")

trim.linkers("/k562-H3k27ac_raw/SRR1514661_1.fastq.gz","/k562-H3k27ac_raw/SRR1514661_2.fastq.gz ", linkers = c("GTTGGATAAG","GTTGGAATGT"), destination.regular = c("regular_m0_1.fastq","regular_m0_2.fastq"), destination.chimeric = c("chimeric_m0_1.fastq","chimeric_m0_2.fastq"),mh=0) fqlist<-c("regular_m0_1.fastq","regular_m0_2.fastq","chimeric_m0_1.fastq","chimeric_m0_2.fastq") align_reads(fqlist, bowtieidex, bowtieCMD)
process.sam("regular_m0_1.sam","regular_m0_2.sam",PET.strand.info = TRUE, remove.old.sam = TRUE)

process.sam("chimeric_m0_1.sam","chimeric_m0_2.sam",PET.strand.info = FALSE)
call.peaks("macs2", c("regular_m0_1_processed.sam", "regular_m0_2_processed.sam","chimeric_m0_1_processed.sam", "chimeric_m0_2_processed.sam"), gsize = "hs", chr.include = "all")
count.interactions("regular_m0_1_processed.sam", "regular_m0_2_processed.sam", "chimeric_m0_1_processed.sam", "chimeric_m0_2_processed.sam","macs2_peaks.narrowPeak", "regular_count.txt", "chimeric_count.txt", "anchor_info.txt", distance.strand.file = "PET_distance_strand.txt", ref.genome ="hg19") pop.test("regular_count.txt", "chimeric_count.txt", "anchor_info.txt", "result.txt", ref.genome = "hg19")

CID

Guo Y, Krismer K, Closser M, Wichterle H, Gifford DK. 2019. High resolution discovery of chromatin interactions. Nucleic Acids Res 47: gkz051-.

Command line

java -Xmx32G -jar gem.jar CID --data /ChIA-PET2_mes_mis1.rmdup.bedpe --g mm10.chrom.sizes --micc 2 --out /ChIA-PET2_mes_mis1_CID

java -Xmx32G -jar gem.jar CID --data /ChIA-PET2_k562_mis1.rmdup.bedpe --g mm10.chrom.sizes --micc 2 --out /ChIA-PET2_k562_mis1_CID

cLoops

Cao Y,Chen Z, Chen X, Ai D, Chen G, McDermott J, Huang Y, Xiaoxiao G, Han J-DJ. 2019. Accurate loop calling for 3D genomic data with cLoops. Bioinformatics.

Command line

cLoops –f /ChIA-PET2_mes_mis1.rmdup.bedpe -o /ChIA-PET2_mes_mis1_cLoops -s -eps 500,1000,2000 -minPts 1,3,5

cLoops –f /ChIA-PET2_k562_mis1.rmdup.bedpe -o /ChIA-PET2_k562_mis1_cLoops -s -eps 500,1000,2000 -minPts 1,3,5

ChiaSig

Paulsen J, Rødland EA, Holden L, Holden M, Hovig E. 2014. A statistical model of ChIA-PET data for accurate detection of chromatin 3D interactions. Nucleic Acids Res 42: e143–e143.

Command line

./ChiaSig –C 2 ChIA-PET2_mes_mis1.rmdup.bedpe > ChIA-PET2_mes_mis1_chiasig.bedpe

./ChiaSig –C 2 ChIA-PET2_k562_mis1.rmdup.bedpe > ChIA-PET2_k562_mis1_chiasig.bedpe