Streamlining SLAMseq analysis with ultra-high sensitivity: SlamDunk is a novel, fully automated software tool for automated, robust, scalable and reproducible SLAMseq data analysis.

References:

• Quantification of experimentally induced nucleotide conversions in high-throughput sequencing datasets, Neumann, T., Herzog, V. A. et al. BMC Bioinformatics, 20(1), 258, 2019.

• Slamdunk documentation

• Module Name: slamdunk (see the modules page for more information)
• Multithreaded

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

[user@biowulf]$ sinteractive --cpus-per-task=8 --mem=20g --gres=lscratch:20
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 slamdunk

[user@cn3144 ~]$ cd /lscratch/$SLURM_JOB_ID

[user@cn3144 ~]$ cp /fdb/genome/hg19/chr_all.fa .

[user@cn3144 ~]$ slamdunk all -r chr_all.fa -b ./exampleBAM.bed \
      -o out -t $SLURM_CPUS_PER_TASK ./exampleBAM.bam
slamdunk all
Running slamDunk map for 1 files (8 threads)
.
Running slamDunk sam2bam for 1 files (8 threads)
.
Creating output directory: out/filter
Running slamDunk filter for 1 files (8 threads)
.
[...]

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

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

#!/bin/bash
set -e
module load slamdunk
cd /lscratch/$SLURM_JOB_ID
cp /fdb/genome/hg19/chr_all.fa .
slamdunk all -r chr_all.fa -b ./exampleBAM.bed \
             -o out -t $SLURM_CPUS_PER_TASK ./exampleBAM.bam

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] [--gres=lscratch:#] slamdunk.sh