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
- Module Name: smart (see the modules page for more information)
- Example files in
$SMART_TEST_DATA
Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.
Allocate an interactive session and run the program. Sample session:
[user@biowulf]$ 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