A Hidden Markov ModeleR for ATAC-seq. HMMRATAC splits a single ATAC-seq dataset into nucleosome-free and nucleosome-enriched signals, learns the unique chromatin structure around accessible regions, and then predicts accessible regions across the entire genome.

Reference:

• Tarbell, Evan D., and Tao Liu. "HMMRATAC: a Hidden Markov ModeleR for ATAC-seq." BioRxiv (2019): 306621.

• HMMRATAC GitHub repository
• HMMRATAC Guide

• Module Name: HMMRATAC (see the modules page for more information)
• Tests suggest that HMMRATAC will automatically try to use the number of threads that you allocate, but they are only utilized in short bursts.
• In testing, HMMRATAC used around 3GB of memory for each CPU allocated.
• Environment variables set
  • HMMRATAC_HOME
• HMMRATAC is a java jar file and should be called like so:
• java -jar $HMMRATAC_HOME/HMMRATAC.jar [options and arguments]

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

First, use samtools to prepare a sample.

[user@biowulf ~]$ sinteractive --cpus-per-task=4 --mem=12G --gres=lscratch:10
salloc.exe: Pending job allocation 41216741
salloc.exe: job 41216741 queued and waiting for resources
salloc.exe: job 41216741 has been allocated resources
salloc.exe: Granted job allocation 41216741
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3125 are ready for job
srun: error: x11: no local DISPLAY defined, skipping

[user@cn3125 ~]$ cd /data/$USER/HMMRATAC/testdata

[user@cn3125 testdata]$ ls
ATACseq.bam

[user@cn3125 testdata]$ module load samtools
[+] Loading samtools 1.9  ...

[user@cn3125 testdata]$ samtools sort -@4 -m 1800M -T /lscratch/$SLURM_JOB_ID/ATACseq.bam \
    -o ATACseq.sorted.bam ATACseq.bam
[bam_sort_core] merging from 0 files and 4 in-memory blocks...

[user@cn3125 testdata]$ samtools index -@4 ATACseq.sorted.bam ATACseq.sorted.bam.bai

[user@cn3125 testdata]$ samtools view -H ATACseq.sorted.bam | \
    perl -ne 'if(/^@SQ.*?SN:(\w+)\s+LN:(\d+)/){print $1,"\t",$2,"\n"}' > \
    genome.info

Then use HMMRATAC to analyze the sample. (Note that these --upper and --lower option/argument pairs may not be realistic.)

[user@cn3125 testdata]$ module load HMMRATAC
[+] Loading HMMRATAC  1.2.9  on cn3125
[+] Loading java 12.0.1  ...

[user@cn3125 testdata]$ java -jar $HMMRATAC_HOME/HMMRATAC.jar --upper 100 --lower 2 \
    --bam ATACseq.sorted.bam \
    --index ATACseq.sorted.bam.bai \
    --genome genome.info

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

#!/bin/bash
#SBATCH --job-name="HMMRATAC-test"
#SBATCH --mem=12g
#SBATCH --ntasks=1
#SBATCH --partition=quick
#SBATCH --time=2:0:0
#SBATCH --cpus-per-task=4
#SBATCH --error=/data/$USER/HMMRATAC-test.e
#SBATCH --output=/data/$USER/HMMRATAC-test.o

module load HMMRATAC
cd /data/$USER/HMMRATAC/testdata

java -jar $HMMRATAC_HOME/HMMRATAC.jar \
    -b ATACseq.sorted.bam \
    -i ATACseq.sorted.bam.bai \
    -g genome.info

Submit this job using the Slurm sbatch command.

[user@biowulf ~]$ sbatch HMMRATAC.sh

Create a swarmfile (e.g. HMMRATAC.swarm). For example:

java -jar $HMMRATAC_HOME/HMMRATAC.jar -b 1.sorted.bam -i 1.sorted.bam.bai -g 1.info
java -jar $HMMRATAC_HOME/HMMRATAC.jar -b 2.sorted.bam -i 2.sorted.bam.bai -g 2.info
java -jar $HMMRATAC_HOME/HMMRATAC.jar -b 3.sorted.bam -i 3.sorted.bam.bai -g 3.info
java -jar $HMMRATAC_HOME/HMMRATAC.jar -b 4.sorted.bam -i 4.sorted.bam.bai -g 4.info

Submit this job using the swarm command.

[user@biowulf ~]$ swarm -f HMMRATAC.swarm [-g #] [-t #] --module HMMRATAC