StaticSection Aggregation

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   October 4th, 2021 at 3:29pm

Aggregation

Pairs are merged and aggregated with pairix version 0.3.3. Pairs files are then converted to mcool via cooler version 0.8.5.

Merging:

  • There is no merging of sequencing replicates. Processing is performed separately for each sequencing replicate.
  • Biological replicates are merged using the same method as used by the Hi-C processing pipeline. That is,
  • Biological replicates are merged after the duplicate removal step, since PCR duplication events happen independently in each replicate.
  • Merging is performed on pairs files using run-merge-pairs.sh.
  • 4DN DCIC provides a merged output as a merged pairs file.

File Format Conversion:

  • mcool files are contact matrices containing multiple resolutions which can be visualized in HiGlass.
  • The 4DN standard resolutions for mcool files are: 1kb, 2kb, 5kb, 10kb, 25kb, 50kb, 100kb, 250kb, 500kb, 1Mb, 2.5Mb, 5Mb, 10Mb.

Source files (v1.1.1_dcic_4):

  • Workflow: https://data.4dnucleome.org/workflows/4DNWFMRGIPC1/
  • CWL: https://github.com/4dn-dcic/iMARGI-Docker/blob/v1.1.1_dcic_4/src/cwl/imargi-processing-pairs.cwl
  • Docker (for merging only): https://github.com/4dn-dcic/docker-4dn-hic/tree/v43