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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

References

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