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🔬 Advanced Modes

MosaiCatcher supports several advanced execution modes for specialized analyses.

ArbiGent mode

Genotype a given list of positions specified in a BED file.

Available from v1.9.0+.

Setup

Set the arbigent=True config parameter. An alternative pipeline branch will execute with results targeted for ArbiGent.

Command

snakemake \
    --cores <N> \
    --config \
        data_location=<INPUT_DATA_FOLDER> \
        arbigent=True \
    --profile workflow/snakemake_profiles/local/conda_singularity/

Custom BED file

A default BED file is provided at: workflow/data/arbigent/manual_segmentation.bed

Specify a custom BED file by setting the arbigent_bed_file parameter:

--config arbigent_bed_file=<path/to/custom.bed>

Note

If you modify the chromosome list (e.g., exclude chrX and chrY), MosaiCatcher automatically extracts only matching rows from the BED file.

scNOVA mode

Determine nucleosome occupancy associated with SV calls.

Available from v1.9.2+.

Warning

Following Anaconda licensing changes at EMBL, scNOVA can only run with singularity profiles that have pre-built conda environments.

Two-step workflow

Step 1: Generate SV calls

Run MosaiCatcher normally to generate initial SV calls and subclonality data.

Step 2: Prepare subclonality file

Create a TSV file at: <DATA_LOCATION>/<SAMPLE>/scNOVA_input_user/input_subclonality.txt

Format (tab-separated):

Filename             Subclonality
TALL3x1_DEA5_PE20406 clone2
TALL3x1_DEA5_PE20414 clone2
TALL3x1_DEA5_PE20415 clone1
TALL3x1_DEA5_PE20416 clone1
TALL3x1_DEA5_PE20417 clone1

Clone identifiers must follow the format clone<N>.

Step 3: Run scNOVA analysis

snakemake \
    --cores <N> \
    --config \
        data_location=<INPUT_DATA_FOLDER> \
        scNOVA=True \
    --profile workflow/snakemake_profiles/local/conda_singularity/

Multistep normalization

Apply advanced normalization (library size, GC correction, Variance Stabilizing Transformation) for both visualization and SV calling.

Available from v2.1.0+.

For visualization only

snakemake \
    --cores <N> \
    --config \
        data_location=<INPUT_DATA_FOLDER> \
        multistep_normalisation=True \
    --profile workflow/snakemake_profiles/local/conda_singularity/

For SV calling

snakemake \
    --cores <N> \
    --config \
        data_location=<INPUT_DATA_FOLDER> \
        multistep_normalisation=True \
        multistep_normalisation_for_SV_calling=True \
    --profile workflow/snakemake_profiles/local/conda_singularity/

Warning

multistep_normalisation_for_SV_calling is mutually exclusive with hgsvc_based_normalized_counts.

BreakpointR integration

Compute breakpoints on Strand-Seq data (David Porubsky).

Enable with the breakpointr=True parameter.

Stop after BreakpointR execution with breakpointr_only=True.

scTRIP multiplot

Advanced visualization module by Marco Cosenza (requires separate repository access).

Available from v2.2.2+.

Setup

Clone the scTRIP multiplot repository into: workflow/scripts/plotting/scTRIP_multiplot

(Contact Marco Cosenza for private repository access)

Enable

--config scTRIP_multiplot=True

Or set scTRIP_multiplot: true in config/config.yaml.

Output

Example multiplot visualization available in Outputs.

IGV tracks upload

Load MosaiCatcher results in the Integrative Genomics Viewer (IGV).

Steps

  1. Start IGV - Launch the IGV application
  2. Open session - Go to File > Open Session
  3. Navigate - Go to: <OUTPUT>/plots/IGV/
  4. Select - Choose <SAMPLE>_IGV_session.xml

Automatic setup

The reference genome set during MosaiCatcher execution automatically loads, along with Watson/Crick and SV tracks for each cell.

For report generation, see Quick Start.