NucleoATAC is a software for nucleosome calling using ATAC-seq. It can identify the rotational and translational positions of nucleosomes with up to base-pair resolution and provide quantitative measures of nucleosome occupancy.

• NucleoATAC GitHub page
• NucleoATAC documentation

• Module Name: NucleoATAC (see the modules page for more information)
• Unusual environment variables set
  • NUCLEOATAC_HOME  installation directory
  • NUCLEOATAC_BIN       executable directory
  • NUCLEOATAC_SRC       source code directory
  • NUCLEOATAC_DATA  sample data directory

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive --cpus-per-task=16 --mem=32g --gres=lscratch:10
[user@cn3200 ~]$module load NucleoATAC 
[+] Loading singularity  4.0.1  on cn3200
[+] Loading nucleoatac  0.3.4

[user@cn3200 ~]$ cp -r $NUCLEOATAC_DATA/* .
[user@cn3200 ~]$ nucleoatac run -h 
Command run:  /usr/local/apps/NucleoATAC/0.3.4/bin/nucleoatac run -h
nucleoatac version 0.3.4
start run at: 2019-05-29 14:14
usage: nucleoatac run [-h] --bed bed_file --bam bam_file --out output_basename
                      --fasta genome_seq [--pwm Tn5_PWM] [--cores num_cores]
                      [--write_all]

optional arguments:
  -h, --help            show this help message and exit

Required:
  Necessary arguments

  --bed bed_file        Regions for which to do stuff.
  --bam bam_file        Accepts sorted BAM file
  --out output_basename
                        give output basename
  --fasta genome_seq    Indexed fasta file

Bias calculation parameters:

  --pwm Tn5_PWM         PWM descriptor file. Default is Human.PWM.txt included
                        in package

General options:

  --cores num_cores     Number of cores to use
  --write_all           write all tracks

[user@cn3200 ~]$ git clone https://github.com/GreenleafLab/NucleoATAC 
[user@cn3200 ~]$ cd NucleoATAC/example
[user@cn3200 ~]$ nucleoatac run \
                        --bed example.bed \
                        --bam example.bam \
                        --fasta sacCer3.fa \
                        --out test_output \
                        --cores 8 
Command run:  /opt/conda/envs/nucleoatac/bin/nucleoatac run --bed example.bed --bam example.bam --fasta sacCer3.fa --out test_output --cores 8
nucleoatac version 0.3.4
start run at: 2024-03-05 11:47
---------Step1: Computing Occupancy and Nucleosomal Insert Distribution---------
Making figure
---------Step2: Processing Vplot------------------------------------------------
---------Step3: Obtaining nucleosome signal and calling positions---------------
---------Step4: Making combined nucleosome position map ------------------------
---------Step5: Calling NFR positions-------------------------------------------
end run at: 2024-03-05 11:48

[user@cn3200 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$