Quick Links Documentation Notes Interactive job Batch job Swarm of jobs

Modbamtools is a set of tools to manipulate and visualize DNA/RNA base modification data that are stored in bam format. htslib has included a support for parsing modified base tags from alignment files (MM and ML). These tags have provided a better/efficient way for storing modification data inside alignment files.

References:

• ProfileRoham Razaghi, ProfilePaul W. Hook, ProfileShujun Ou, ProfileMichael C. Schatz, ProfileKasper D. Hansen, ProfileMiten Jain, ProfileWinston Timp Modbamtools: Analysis of single-molecule epigenetic data for long-range profiling, heterogeneity, and clustering Biorxiv

• modbamtools Main Site:Main Site
• modbamtools Main Site:Tutorial

• Module Name: modbamtools (see the modules page for more information)
• Environment variables set
  • $MODBAMTOOLS_TEST_DATA #include bam, bigwig, gtf and bed files.

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

[user@biowulf]$ sinteractive --cpus-per-task=2 --mem=2G
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 modbamtools
[user@cn3144 ]$ cp -r ${MODBAMTOOLS_TEST_DATA:-none}/* .
[user@cn3144 ]$ cd modbamtools_tutorial_files
[user@cn3144 ]$ modbamtools plot -r chr20:58815000-58895000 \
     --gtf gencode.v38.annotation.sorted.gtf.gz \
     --out . \
     --prefix gm12878_GNAS \
     --samples GM12878 \
     --track-titles Genes\
     gm12878_ul_sup_megalodon_HP_chr20.bam

[user@cn3144]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

This will generate gm12878_GNAS.html:

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

#!/bin/bash
#SBATCH --cpus-per-task=2
#SBATCH --mem=2G
#SBATCH --time=2:00:00
#SBATCH --partition=norm

set -e
module load modbamtools
cp -r ${MODBAMTOOLS_TEST_DATA:-none}/* .
cd modbamtools_tutorial_files
modbamtools plot -r chr20:58815000-58895000 \
    --gtf gencode.v38.annotation.sorted.gtf.gz \
    --out . \
    --hap \
    --prefix gm12878_GNAS \
    --samples GM12878 \
    --track-titles Genes\
    gm12878_ul_sup_megalodon_HP_chr20.bam 

Submit the job:

sbatch modbamtools.sh

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

       modbamtools plot xxx
       modbamtools plot xxx
    

Submit this job using the swarm command.

swarm -f job.swarm [-g #] --module modbamtools

where

-g #	Number of Gigabytes of memory required for each process (1 line in the swarm command file)
--module	Loads the module for each subjob in the swarm