ASPEN

Atac Seq PipEliNe :

CCBR recommends ASPEN to effectively analyze ATAC-seq datasets on the BIOWULF HPC system at the NIH.

QuickStart guide

bash module load ccbrpipeliner/7

bash aspen --help

```bash

Welcome to

|| [ |] |_ |\ | | | ] | | | | v1.0.6

ATACSeq Analysis PipEliN_e

This pipeline was built by CCBR (https://bioinformatics.ccr.cancer.gov/ccbr) Please contact Vishal Koparde for comments/questions (vishal.koparde@nih.gov)

Here is a list of genome supported by aspen:

• hg19 [Human]
• hg38 [Human]
• mm10 [Mouse]
• mmul10 [Macaca mulatta(Rhesus monkey) or rheMac10]
• bosTau9 [Bos taurus(cattle)]

aspen calls peaks using the following tools:

• MACS2
• Genrich [RECOMMENDED FOR USE]

USAGE: bash /data/CCBR_Pipeliner/Pipelines/ASPEN/.v1.0.6/aspen -w/--workdir= -m/--runmode=

Required Arguments: 1. WORKDIR : [Type: String]: Absolute or relative path to the output folder with write permissions.

1. RUNMODE : [Type: String] Valid options:
   • init : initialize workdir
   • dryrun : dry run snakemake to generate DAG
   • run : run with slurm
   • runlocal : run without submitting to sbatch ADVANCED RUNMODES (use with caution!!)
   • unlock : unlock WORKDIR if locked by snakemake NEVER UNLOCK WORKDIR WHERE PIPELINE IS CURRENTLY RUNNING!
   • reconfig : recreate config file in WORKDIR (debugging option) EDITS TO config.yaml WILL BE LOST!
   • reset : DELETE workdir dir and re-init it (debugging option) EDITS TO ALL FILES IN WORKDIR WILL BE LOST!
   • printbinds: print singularity binds (paths)
   • local : same as runlocal

Optional Arguments:

--genome|-g : genome eg. hg38 --manifest|-s : absolute path to samples.tsv. This will be copied to output folder (--runmode=init only) --help|-h : print this help

Example commands: bash /data/CCBRPipeliner/Pipelines/ASPEN/.v1.0.6/aspen -w=/my/output/folder -m=init bash /data/CCBRPipeliner/Pipelines/ASPEN/.v1.0.6/aspen -w=/my/output/folder -m=dryrun bash /data/CCBR_Pipeliner/Pipelines/ASPEN/.v1.0.6/aspen -w=/my/output/folder -m=run

VersionInfo: python : python/3.10 snakemake : snakemake pipelinehome : /data/CCBRPipeliner/Pipelines/ASPEN/.v1.0.6 git commit/tag : f4366158ad972bc667422dcd4783bd69fa041556 v1.0.6 aspen_version : v1.0.6

```

Visit ASPEN documentation for details.

For comments/suggestions/advice please reach out to Vishal Koparde or CCBR_Pipeliner. You can also open a new issue here.

Back to Top