Run

Run pipeline:¶

Simply submit the pipeline as a slurm job:

sbatch isomiR.sh <ExperimentName> "<Options>"

Example run:

sbatch isomiR.sh Name "--trimmer Qiagen --MinLen 18 --consensus motif-consensus.fa --index hg38"

List of options.

• --trimmer : Trimmer used. Default is Qiagen.

  • Qiagen
  • Illumina
  • NEB
  • GuLab
  • None

• --MinLen: Minimum length for trimming. Requires an integer. Default is 18.

• --consensus : alternative consensus file.

• --index : Index for profiling. Currently available:

  • hg38
  • mm39

• --sRNAprofiling : Yes or No. No skips this step.

• --QuagmiR : Yes or No. No skips this step.