ASPEN

Atac Seq PipEliNe :

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

QuickStart guide

module load ccbrpipeliner

Note: This is illustrative example output captured at doc-writing time — exact values (e.g. pipeline_home, git commit/tag, aspen_version) will differ depending on which ASPEN version/branch is installed at your site. Run aspen --help yourself to see the current values for your installation.

aspen --help

##########################################################################################

Welcome to

╔══════════════════════════════════╗
║  ASPEN PIPELINE                  ║
║  v1.3.0                          ║
╚══════════════════════════════════╝

ATAC-Seq Analysis Pipeline

##########################################################################################

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)]
  * hs1           [Human T2T-CHM13]
  * hs1_chrR      [Human T2T-CHM13 + chrR rDNA unit]

aspen calls peaks using the following tools:

 * MACS2
 * Genrich        [RECOMMENDED FOR USE]

USAGE:
  bash /data/CCBR_Pipeliner/Pipelines/ASPEN/release/1.3.0/aspen -w/--workdir=<WORKDIR> -m/--runmode=<RUNMODE>

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

2.  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/CCBR_Pipeliner/Pipelines/ASPEN/release/1.3.0/aspen -w=/my/output/folder -m=init
  bash /data/CCBR_Pipeliner/Pipelines/ASPEN/release/1.3.0/aspen -w=/my/output/folder -m=dryrun
  bash /data/CCBR_Pipeliner/Pipelines/ASPEN/release/1.3.0/aspen -w=/my/output/folder -m=run

##########################################################################################

VersionInfo:
  python          : python/3.10
  snakemake       : snakemake
  pipeline_home   : /data/CCBR_Pipeliner/Pipelines/ASPEN/release/1.3.0
  git commit/tag  : 8d197d39927be3f60558911bd8b2756f36835deb    v1.3.0
  aspen_version   : v1.3.0

##########################################################################################

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

---