Quick Links Batch job on Biowulf Swarm of jobs on Biowulf Documentation

MOdel based Analysis of Bisulfite Sequencing data

A comprehensive, accurate and efficient solution for analysis of large scale base-resolution DNA methylation data, bisulfite sequencing or single molecule direct sequencing.

• MOABS on Google Code

• Sun, Deqiang, et al. "MOABS: model based analysis of bisulfite sequencing data." Genome biology 15.2 (2014): 1.

Write a configuration file as described in the moabs manual and set up a batch script along the following lines:

#!/bin/bash
# file called myjob.bat

module load moabs
cd /path/to/moabs/data
moabs -cf myrun.cfg

Submit this job with:

[user@biowulf ~]$ sbatch myjob.bat

Set up a swarm command file containing one line for each of your MOABS runs. Typically, only the input sequence name will change from line to line, but in the example below, different parameters are being applied to each sequence.

Sample swarm command file

# --------file myjobs.swarm----------
moabs -cf myrun1.cfg
moabs -cf myrun2.cfg
moabs -cf myrun3.cfg
....
moabs -cf myrunN.cfg
# -----------------------------------

Submit this set of runs to the batch system by typing

[user@biowulf ~]$ swarm --module moabs -f myjobs.swarm

For details on using swarm see Swarm on Biowulf.