ngsplot is an easy-to-use global visualization tool for next-generation sequencing data.

References:

• Shen L, Shao N, Liu X and Nestler E. ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases. BMC Genomics, 15, 284 (2014).

• https://code.google.com/p/ngsplot/

• Module Name: ngsplot (see the modules page for more information)
• Multithreaded
• Environment variables set
  • NGSPLOT_HOME
  • NGSPLOT_EXAMPLES
• Example files in NGSPLOT_EXAMPLES

Memory Errors

When ngsplot is run without adequate memory allocation, you may get the following errors:

Error: dims [product 89082] do not match the length of object [0]

or

Error in (result.matrix + result.pseudo.rpm)/(bkg.matrix + bkg.pseudo.rpm) :

Typically ngsplot will require at least 4gb of memory.

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

[user@biowulf]$ sinteractive --cpus-per-task=8 --mem=20g
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 ngsplot
[user@cn3144 ~]$ cp $NGSPLOT_EXAMPLES/* .
[user@cn3144 ~]$ ngs.plot.r -G hg19 -R tss -C hesc.H3k4me3.1M.bam -O k4.test -P $SLURM_CPUS_PER_TASK
Loading R libraries.....Done
Configuring variables...Done
Analyze bam files and calculate coverage............................................................................................................................................................................................................................................Done
Plotting figures...Done
Saving results...Done
Wrapping results up...Done
All done. Cheers!
[user@cn3144 ~]$ ls *.pdf
hesc.H3k4me3.tss.avgprof.pdf  hesc.H3k4me3.tss.heatmap.pdf
[user@cn3144 ~]$ display hesc.H3k4me3.tss.avgprof.pdf
[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

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

#!/bin/bash
module load ngsplot
ngs.plot.r -G hg19 -R tss -C hesc.H3k4me3.1M.bam -O hesc.H3k4me3.tss -T H3K4me3 -L 3000 -FL 300 -P $SLURM_CPUS_PER_TASK

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] ngsplot.sh

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

ngs.plot.r -G hg19 -R tss -C sample1.bam -O sample1.tss -T H3K4me3_1 -L 3000 -FL 300 -P $SLURM_CPUS_PER_TASK
ngs.plot.r -G hg19 -R tss -C sample2.bam -O sample2.tss -T H3K4me3_2 -L 3000 -FL 300 -P $SLURM_CPUS_PER_TASK
ngs.plot.r -G hg19 -R tss -C sample3.bam -O sample3.tss -T H3K4me3_3 -L 3000 -FL 300 -P $SLURM_CPUS_PER_TASK
ngs.plot.r -G hg19 -R tss -C sample4.bam -O sample4.tss -T H3K4me3_4 -L 3000 -FL 300 -P $SLURM_CPUS_PER_TASK

Submit this job using the swarm command.

swarm -f ngsplot.swarm [-g #] [-t #] --module ngsplot