DNAscent Help

DNAscent is software designed to detect the base analogues BrdU and EdU in single molecules of DNA sequenced on the Oxford Nanopore platform. In an experimental setup where BrdU and EdU are incorporated into nascent DNA by replication forks, this software can be used to answer questions that were traditionally answered by DNA fibre analysis. DNAscent can also call the genomic positions of stalled and stressed replication forks for use as a replication stress assay.

• https://github.com/MBoemo/DNAscent

A copy of DNAScent 4.1.1 container has been downloaded to /nobackup/shared/containers on Comet - it is recommended that you use this newer, supported method to run DNAscent.

To call DNAscent, a simple example is given below:

#!/bin/bash

# Load the apptainer software module
module load apptainer

# Define the location of the DNAscent container file
DNASCENT_SIF_FILE=/nobackup/shared/containers/mboemo_dnascent_dnascent.sif

# Use apptainer to run the container file, in this example running the 'detect' subcomponent of dnascent
apptainer run $DNASCENT_SIF_FILE detect

This version should run on any compute node. If you want to run on a GPU-node and take advantage of the Nvidia accelerated compute methods, add the -nv flag to the apptainer command and remember to allocate a GPU in your Slurm job script:

#!/bin/bash

# Load the apptainer software module
module load apptainer

# Define the location of the DNAscent container file
DNASCENT_SIF_FILE=/nobackup/shared/containers/mboemo_dnascent_dnascent.sif

# Use apptainer to run the container file, in this example running the 'detect' subcomponent of dnascent
apptainer -nv run $DNASCENT_SIF_FILE detect

Follow the Official documentation for full instructions on how to use DNAscent. In the official instructions any time it refers to Singularity you can assume that the same applies to Apptainer. You do not need to build anything from source - it is all ready for you to use in the container.

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