SMART on Biowulf & Helix
Description
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.
There may be multiple versions of SMART available. An easy way of selecting the version is to use modules. To see the modules available, type
module avail smart
To select a module use
module load smart/[version]
where [version] is the version of choice.
Environment variables set
-
$PATH -
$SMART_TEST_DATA
References
- H. Liu, X. Liu, S. Zhang, J. Lv, S. Li, S. Shang, S. Jia, Y. Wei, F. Wang, J. Su et al. Systematic identification and annotation of human methylation marks based on bisulfite sequencing methylomes reveals distinct roles of cell-type-specific hypomethylation in regulation of cell identify genes. Nucleic Acids Research 2016, 44:75-94. PubMed | PMC | Journal
Documentation
Interactive job on Biowulf
Allocate an interactive session with sinteractive and use as shown below.
biowulf$ sinteractive --mem=10g salloc.exe: Pending job allocation 30611331 salloc.exe: job 30611331 queued and waiting for resources salloc.exe: job 30611331 has been allocated resources salloc.exe: Granted job allocation 30611331 salloc.exe: Waiting for resource configuration salloc.exe: Nodes cn2694 are ready for job srun: error: x11: no local DISPLAY defined, skipping
For SMART 1.X
node$ module load smart
[+] Loading smart 1.4.2.20150517
node$ mkdir smart_test
node$ cd smart_test/
node$ cp -r $SMART_TEST_DATA/* .
node$ ll
total 8.0K
drwxr-xr-x 2 wresch staff 4.0K Jan 4 15:09 BSSeq_fortest
drwxr-xr-x 2 wresch staff 4.0K Jan 4 15:09 CLoc_hg19_fortest
node$ # BSSeq_fortest contains the wiggle files with the quantified methylation levels in
# different cell types for two small chunks of chr3 and chr6.
node$ SMART -n test BSSeq_fortest CLoc_hg19_fortest
/spin1/users/wresch/test_data/smart/smart_test/test20170104150951/
2017-01-04 15:09:51 Project test Start
[...snip...]
2017-01-04 15:09:53 ********************Project Summary******************
2017-01-04 15:09:53 Chromesomes : chr3,chr6
2017-01-04 15:09:53 Sample Number : 6
2017-01-04 15:09:53 Sample Names : Gastric,Ovary,H1,Thymus,IMR90,Spermatozoa
2017-01-04 15:09:53 Number of total Cytosines in all chromesomes: 46643
[...snip...]
2017-01-04 15:09:53 Project test Finished !
node$ ll
total 12K
drwxr-xr-x 2 user staff 4.0K Jan 4 15:09 BSSeq_fortest
drwxr-xr-x 2 user staff 4.0K Jan 4 15:09 CLoc_hg19_fortest
drwxr-xr-x 6 user staff 4.0K Jan 4 15:09 test20170104150951
node$ tree test20170104150951/
test20170104150951/
|-- [user 4.0K] FinalResults
| |-- [user 9.5K] 1SmallSegmentBed.txt.gz
| |-- [user 1.3K] 2MergedSegmentBed.txt.gz
| |-- [user 4.1K] 3MergedSegment.txt
| |-- [user 5.6K] 4MergedSegmentwithmethylation.txt
| |-- [user 2.2K] 5MergedHighLowSpeSegmentwithspecificity.txt
| `-- [user 1.2K] 6CellTypeSpecificMethymarkPvalue.txt
|-- [user 4.0K] MethylationSegment
| |-- [user 4.0K] GenomeSegment
| | |-- [user 12K] chr3.txt
| | `-- [user 11K] chr6.txt
| |-- [user 4.0K] GenomeSegmentMethy
| | |-- [user 7.5K] chr3.txt.gz
| | `-- [user 7.6K] chr6.txt.gz
| `-- [user 4.0K] MergedGenomeSegment
| |-- [user 3.3K] chr3.txt
| `-- [user 6.0K] chr6.txt
|-- [user 4.0K] MethylationSpecificity
| |-- [user 26K] chr3.txt.gz
| |-- [user 23K] chr6.txt.gz
| `-- [user 13K] MethylationSpecificity.wig.gz
|-- [user 3.6K] ProjectReport.txt
`-- [user 4.0K] SplitedMethy
|-- [user 4.0K] chr3
| |-- [user 8.4K] chr3_Gastric.wig.gz
| |-- [user 8.0K] chr3_H1.wig.gz
| |-- [user 8.2K] chr3_IMR90.wig.gz
| |-- [user 8.3K] chr3_Ovary.wig.gz
| |-- [user 6.7K] chr3_Spermatozoa.wig.gz
| `-- [user 8.3K] chr3_Thymus.wig.gz
`-- [user 4.0K] chr6
|-- [user 7.0K] chr6_Gastric.wig.gz
|-- [user 6.8K] chr6_H1.wig.gz
|-- [user 7.5K] chr6_IMR90.wig.gz
|-- [user 7.1K] chr6_Ovary.wig.gz
|-- [user 6.4K] chr6_Spermatozoa.wig.gz
`-- [user 6.6K] chr6_Thymus.wig.gz
node$ exit
biowulf$
For SMART 2.x - note the changed command line interface
node$ module load smart [+] Loading smart 2.1.5 node$ mkdir example node$ cp -r $SMART_TEST_DATA/* example node$ SMART -t DeNovoDMR -o ./testout MethylMatrix_Test.txt [...snip...] node$ 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
Batch job on Biowulf
Create a batch script similar to the following example:
#! /bin/bash # this file is smart.batch module load smart/1.4.2.20150517 || exit 1 SMART -n test BSSeq_fortest CLoc_hg19_fortest
Submit to the queue with sbatch:
biowulf$ sbatch --mem=5g smart.batch
