demux_doublet_sim
Repository for Nextflow pipeline used in demuxSNP demultipelxing paper
Overall workflow
- Simulate doublets
- Benchmark methods
- Experiments 1: Vary doublet rate
- Experiment 2: Vary SNP subsetting
Inputs
Most inputs are specified in nextflow.config:
container__souporcell: path to souporcell apptainer image, ideally at top level of project.
bam_path: Path to demultiplexed bam files.
barcodes_path: Path to demultiplexed barcodes.
tenx: Path to barcodes.tsv, features.tsv and matrix.mtx files from multiplexed 10X output.
common_variants: common variants e.g. from 1K genome project.
ref: path to reference genome, ideally in data/input directory.
Doublet simulation parameters are specified in params_ccrcc.csv The workflow caters for subsampling (also specified in params_ccrcc.csv) although this was not explored in the paper.
Outputs
Folder for each simulated scenario (e.g. seed, % doublets, number of genes used to subset) SingleCellExperiment object in each demuxSNP folder.
Known issues
Input files used by souporcell/apptainer need to be stored below the image. Apptainer must be bound to the project directory (variable in nextflow.config).
Version History
0.99.1 (latest) Created 16th Sep 2024 at 15:22 by Michael Lynch
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0.99.0 (earliest) Created 10th Sep 2024 at 10:35 by Michael Lynch
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Additional credit
Leverages scripts developed by Weber et al (2021) DOI: https://doi.org/10.1093/gigascience/giab062
Submitter
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Created: 10th Sep 2024 at 10:35
Last updated: 16th Sep 2024 at 15:22
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