CutRunTools2 is a major update of CutRunTools, including a set of new features specially designed for CUT&RUN and CUT&Tag experiments. Both of the bulk and single-cell data can be processed, analyzed and interpreted.

References:

• Fulong Yu, Vijay G Sankaran, Guo-Cheng YuanCUT&RUNTools 2.0:a pipeline for single-cell and bulk-level CUT&RUN and CUT&Tag data analysis Bioinformatics, 2021 PubMed |  Journal

• CutRunTools2 Github:Github

• Module Name: CutRunTools2 (see the modules page for more information)
• Some steps of CutRunTools2 will be run locally, so please make a copy of those programs to your local directory with (this only needs to be done once):

  cp -r ${CutRunTools_TEST_DATA:-none}/* .

• CutRunTools2 needs config JSON file as input, please edit the software_config (only edit the line with apptest1), input_output, and motif_finding to match your username with working path according. This is an example for bulk-config.json:

  {
      "software_config": {
          "Rscriptbin": "/usr/bin",
          "pythonbin": "/opt/conda/envs/app/bin",
          "perlbin": "/opt/conda/envs/app/bin",
          "javabin": "/usr/bin",
          "bowtie2bin": "/opt/conda/envs/app/bin",
          "samtoolsbin": "/opt/conda/envs/app/bin",
          "macs2bin": "/opt/conda/envs/app/bin",
          "memebin": "/opt/conda/envs/meme/bin",
          "bedopsbin": "/opt/conda/envs/app/bin",
          "bedtoolsbin": "/opt/conda/envs/app/bin",
          "path_deeptools": "/opt/conda/envs/app/bin",
          "path_parallel": "/opt/conda/envs/app/bin",
          "path_tabix": "/opt/conda/envs/app/bin",
          "bt2idx": "/fdb/igenomes/Homo_sapiens/UCSC/hg38/Sequence/Bowtie2Index",
          "genome_sequence": "/fdb/igenomes/Homo_sapiens/UCSC/hg38/Sequence/WholeGenomeFasta/genome.fa",
          "extratoolsbin": "/data/apptest1/cutruntools2/install",
          "extrasettings": "/data/apptest1/cutruntools2/install",
          "kseqbin": "/opt/CUT-RUNTools-2.0/install",
          "adapterpath": "/opt/CUT-RUNTools-2.0/adapters",
          "trimmomaticbin": "/data/apptest1/cutruntools2/install",
          "picardbin": "/data/apptest1/cutruntools2/install",
          "picardjarfile": "picard-2.8.0.jar",
          "trimmomaticjarfile": "trimmomatic-0.36.jar",
  	"makecutmatrixbin": "/opt/conda/envs/app/bin"
      },
      "input_output": {
          "fastq_directory": "/data/apptest1/cutruntools2/exampleData",
          "workdir": "/data/apptest1/cutruntools2/bulk-example-test",
          "fastq_sequence_length": "42",
          "organism_build": "hg38",
          "spike_in": "FALSE",
          "spike_in_norm": "FALSE",
          "spikein_scale": "10000",
          "frag_120": "TRUE",
          "peak_caller": "macs2",
          "dup_peak_calling": "FALSE",
          "cores": "8",
          "experiment_type": "CUT&RUN"
      },
      "motif_finding": {
          "num_bp_from_summit": "100",
          "num_peaks": "1000",
          "total_peaks": "2000",
          "motif_scanning_pval": "0.0005",
          "num_motifs": "10"
      }
  }
  
  
  	

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive --ntasks=8 --cpus-per-task=6 --mem=20G --nodes=1
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load CutRunTools2
[user@cn3144 ~]$ mkdir /data/$USER/cutruntools2/
[user@cn3144 ~]$ cd /data/$USER/cutruntools/
[user@cn3144 ~]$ cp -r ${CutRunTools_TEST_DATA:-none}/* .
[user@cn3144 ~]$ python ./validate.py bulk-config.json --ignore-input-output --software
[user@cn3144 ~]$ bash run_bulkModule.sh bulk-config.json test1 &>test1_bulk.out

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. cutruntools2_sc.sh). For example:

#!/bin/bash
set -e
module load CutRunTools2
cd /data/$USER/cutruntools2/
cp -r ${CutRunTools_TEST_DATA:-none}/* .
python ./validate.py sc-config.json --ignore-input-output --software
bash run_scModule.sh sc-config.json

Submit this job using the Slurm sbatch command.

sbatch --ntasks=8 --cpus-per-task=6 --mem=70G --nodes=1 cutruntools2_sc.sh