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. 2022 May 2;13:2365. doi: 10.1038/s41467-022-29697-4

Table 2.

4D Nucleome analysis pipelines.

Pipeline Steps Software Available file formats CWL/WDL filename
Hi-C1 Alignment bwa-mem .bam bwa-mem.cwl
Filtering pairtools .pairs hi-c-processing-bam.cwl
Merging replicates & matrix aggregation cooler .hic, .mcool hi-c-processing-pairs.cwl
MARGI2 Alignment bwa-mem .bam imargi-processing-fastq.cwl
Filtering pairtools .pairs imargi-processing-bam.cwl
Merging replicates & matrix aggregation cooler .mcool imargi-processing-pairs.cwl
Repli-seq3 Alignment bwa-mem .bam repliseq-parta.cwl
Filtering samtools -
Binning & aggregation bedtools .bw, .bg
CUT&RUN4 Alignment & filtering bowtie2, Picard, samtools, bedtools .bam, .bedpe cut-and-run-processing.cwl
Peak calling SEACR .bw, .bg, .bed cut-and-run-postaln.cwl
ATAC-seq5 Alignment & filtering bowtie2, bedtools .bed atac.wdl
Peak calling MACS2 .bw, .bigbed
ChIP-seq6 Alignment & filtering bwa, bedtools .bed chip.wdl
Peak calling MACS2, SPP .bw, .bigbed
RNA-seq7 Alignment STAR .bam rna-seq-pipeline.wdl
Expression quantification RSEM .tsv
Read coverage STAR .bw

Listed below are (i) subdirectories for Docker images from https://hub.docker.com/r/4dndcic; (ii) subdirectories from github repositories at https://github.com/4dn-dcic/ that hold the CWL or WDL pipeline files; and (iii) subdirectories for more information from https://data.4dnucleome.org/resources/data-analysis/. Note that for the Repliseq pipeline as well as the WDL pipelines from ENCODE, there is only one workflow file for the whole pipeline.

14dn-hic, docker-4dn-hic/tree/v43/cwl, hi_c-processing-pipeline.

2imargi, iMARGI-Docker/tree/v1.1.1_dcic_4/src/cwl, imargi-pipeline.

3repliseq, docker-4dn-repliseq/tree/v16/cwl, repli-seq-processing-pipeline.

4cut-and-run-pipeline, docker-4dn-cut-and-run-pipeline/tree/v1/cwl, cut-and-run-pipeline.

5encode-atacseq, atac-seq-pipeline, atacseq-processing-pipeline.

6encode-chipseq, chip-seq-pipeline2, chipseq-processing-pipeline.

7encode-rnaseq, rna-seq-pipeline, rnaseq-processing-pipeline information.