Hicexplorer

Introduction

Hicexplorer is a set of tools to process, normalize and visualize Hi-C data.

For more information, please check:
BioContainers: https://biocontainers.pro/tools/hicexplorer
Home page: https://hicexplorer.readthedocs.io/en/latest/#

Note

Please follow the recommended citation guidelines from the developers when you use the tool in research.

Versions

Cluster

Version(s)

ANVIL

3.7.2

BELL

3.7.2

GAUTSCHI

3.7.2

NEGISHI

3.7.2

SCHOLAR

3.7.2

Commands

  • chicAggregateStatistic

  • chicDifferentialTest

  • chicExportData

  • chicPlotViewpoint

  • chicQualityControl

  • chicSignificantInteractions

  • chicViewpoint

  • chicViewpointBackgroundModel

  • hicAdjustMatrix

  • hicAggregateContacts

  • hicAverageRegions

  • hicBuildMatrix

  • hicCompareMatrices

  • hicCompartmentalization

  • hicConvertFormat

  • hicCorrectMatrix

  • hicCorrelate

  • hicCreateThresholdFile

  • hicDetectLoops

  • hicDifferentialTAD

  • hicexplorer

  • hicFindEnrichedContacts

  • hicFindRestSite

  • hicFindTADs

  • hicHyperoptDetectLoops

  • hicHyperoptDetectLoopsHiCCUPS

  • hicInfo

  • hicInterIntraTAD

  • hicMergeDomains

  • hicMergeLoops

  • hicMergeMatrixBins

  • hicMergeTADbins

  • hicNormalize

  • hicPCA

  • hicPlotAverageRegions

  • hicPlotDistVsCounts

  • hicPlotMatrix

  • hicPlotSVL

  • hicPlotTADs

  • hicPlotViewpoint

  • hicQC

  • hicQuickQC

  • hicSumMatrices

  • hicTADClassifier

  • hicTrainTADClassifier

  • hicTransform

  • hicValidateLocations

Module

You can load the modules by:

module load biocontainers
module load hicexplorer

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run hicexplorer on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -p wholenode        # Partition name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=hicexplorer
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers hicexplorer

# Your hicexplorer workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p cpu         # Partition name
#SBATCH -q normal      # QOS name (optional)
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=hicexplorer
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers hicexplorer

# Your hicexplorer workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p ai          # Partition name
#SBATCH --gres=gpu:1   # Number of GPUs
#SBATCH -q normal      # QOS name (optional)
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=hicexplorer
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers hicexplorer

# Your hicexplorer workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p a100        # Partition name
#SBATCH --gres=gpu:1   # Number of GPUs
#SBATCH --mem=2G       # Memory
#SBATCH -q normal      # QOS name (optional)
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=hicexplorer
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers hicexplorer

# Your hicexplorer workflow...

#!/bin/bash
#SBATCH -A queue     # Queue name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=hicexplorer
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers hicexplorer

# Your hicexplorer workflow...