ASE (alternate splicing events) are identified and quantified using the ASCENT (Alternate SpliCing EveNt Tools) pipeline. This workflow can be used for multi-group multi-contrasts scenarios.
ASCENT currently runs:
NOTE: More ASE tools will be added to ASCENT in the future as and when needed. Please contact Vishal Koparde to make requests to add specific ASE tool(s).
% bash /data/Ziegelbauer_lab/Pipelines/CCBR_ASE/v0.1.1/run
Pipeline Dir: /gpfs/gsfs12/users/Ziegelbauer_lab/Pipelines/CCBR_ASE/v0.1.1
Git Commit/Tag: a41b33007b6063b1d95744808f527a126fb1f0dc v0.1.1
/gpfs/gsfs12/users/Ziegelbauer_lab/Pipelines/CCBR_ASE/v0.1.1/run
--> run CCBR Alternate Splicing Events Pipeline
USAGE:
bash /data/Ziegelbauer_lab/Pipelines/CCBR_ASE/v0.1.1/run -m/--runmode=<RUNMODE> -w/--workdir=<WORKDIR>
Required Arguments:
1. RUNMODE: [Type: String] Valid options:
*) init : initialize workdir
*) run : run with slurm
*) reset : DELETE workdir dir and re-init it
*) dryrun : dry run snakemake to generate DAG
*) unlock : unlock workdir if locked by snakemake
*) runlocal : run without submitting to sbatch
2. WORKDIR: [Type: String]: Absolute or relative path to the output folder with write permissions.
IsoformSwitchAnalyzeR fails if replicates are absent.