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.