====== 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

===== Running from Container =====

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:

   * ''/nobackup/shared/containers/mboemo_dnascent_dnascent.sif''

To simplify the running of DNAscent we have provided a helper script:

   * ''/nobackup/shared/containers/mboemo_dnascent_dnascent.sh''

You should ''source'' this file - either on login to Comet if you are working interactively, or at the start of your sbatch file if submitting a job:

<code lang=bash>
$ source /nobackup/shared/containers/mboemo_dnascent_dnascent.sh
</code>

You can then run commands from inside the container with the ''container.run'' prefix, for example, to run the DNAscent ''detect'' command:

<code lang=bash>
$ source /nobackup/shared/containers/mboemo_dnascent_dnascent.sh
$ container.run detect
</code>

You **don't** need to manually add the ''bind'' options to Apptainer to enable access to the ''/scratch'' and ''/nobackup'' directories - the helper script does that for you.

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 [[started:resource_overview#gpu_cards|remember to allocate a GPU in your Slurm job script]]. If available, the GPU will be passed through to the container automatically.

Follow the [[https://dnascent.readthedocs.io/en/latest/index.html|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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