Biowulf High Performance Computing at the NIH
smart on Biowulf

Specific Methylation Analysis and Report Tool (SMART) uses the signal from bisulfite sequencing experiments across multiple samples to identify genome segments with similar methylation secificities. Inputs are a directory with wiggle files of methylation signal from different samples and a directory containing sequence information for all Cs in the genome to be processed. Segments are merged and classified as having high, low, or no cell type specificity.

References:

  • H. Liu, X. Liu, S. Zhang, J. Lv, S. Li, S. Shang, S. Jia, Y. Wei, F. Wang, J. Su et al. Systematic identification and annotation of human methylation marks based on bisulfite sequencing methylomes reveals distinct roles of cell-type-specific hypomethylation in regulation of cell identify genes. Nucleic Acids Research 2016, 44:75-94. PubMed |  PMC |  Journal
Documentation
Important Notes

Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

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

[user@biowulf]$ sinteractive --mem=10g --gres=lscratch:10
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 smart
[user@cn3144]$ cd /lscratch/$SLURM_JOB_ID
[user@cn3144]$ cp -r $SMART_TEST_DATA/* .
[user@cn3144]$ SMART -t DeNovoDMR -o ./testout MethylMatrix_Test.txt
[...snip...]
[user@cn3144]$ ls -lh testout/DeNovoDMR
-rw-r--r-- 1 user group 396K May 31 15:22 1_DifferMethlCpGs.txt.gz
-rw-r--r-- 1 user group  11K May 31 15:22 2_MergedSegment.bed.gz
-rw-r--r-- 1 user group  12K May 31 15:22 3_MergedSegment.txt.gz
-rw-r--r-- 1 user group  21K May 31 15:22 4_MergedSegmentwithmethylation.txt.gz
-rw-r--r-- 1 user group 8.3K May 31 15:22 5_MergedSegment_GroupSpecificity.txt.gz
-rw-r--r-- 1 user group 3.5K May 31 15:22 6_GroupSpecific_Methylmark.txt.gz
-rw-r--r-- 1 user group 3.8K May 31 15:22 Summary.txt

[user@cn3144]$ SMART -t DeNovoDMR -c Case_control_matrix.txt -o ./testout2 MethylMatrix_Test.txt
[user@cn3144]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf]$

Batch job
Most jobs should be run as batch jobs.

Create a batch input file (e.g. smart.sh) similar to the follwing example:

#! /bin/bash

module load smart/2.2.8 || exit 1
cp -r $SMART_TEST_DATA/* .
SMART -t DMROI -r CpGisland_hg19.bed -o testout3 MethylMatrix_Test.txt

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=2 --mem=10g --time=20 smart.sh