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atlas-deconvolution-references

Snakemake workflow to generate single-cell reference dataset for bulk RNA-seq deconvolution in Atlas

It contains rules for:

  • SeuratObject creation
  • Spliting SeuratObjects into tissues
  • Reducing cell type label granularity
  • Creation of references for deconvolution tools
  • UMAP plots for quality control
  • Creating summary file of references

Prerequisites

  • Snakemake
  • A batch scheduler, LSF or SLURM
  • Set up configuration variables at run_deconvolution_reference_creation.sh
  • Config.yaml with sc experiment accessions as input and tissues that are excluded for accessions (look at example.yaml how that should look like)
  • Download ontology files for UBERON and CL ontology and put in folder files

Run pipeline

bash run_deconvolution_reference_creation.sh

This file contains:

  • definition of variables
  • runs snakemake like this:
snakemake \
  -s $SNAKEFILE  \
  --profile [cluster profile 'lsf' or 'slurm'] \
  --rerun-incomplete \
  --retries 3 \ # if job fails try with more memory
  --use-conda --conda-frontend mamba --keep-going \
  --config atlas_prod=[path/to/atlas_prot_dir]\
  anndata_prod=[path/to/anndata_prot_dir]\
  deconv_ref=[path/to/desination/of/reference_library] \

For SLURM profile, add --slurm.

  • checks if references for organims parts are generated more than once and returns duplicated organism parts which can then be included in config.yaml.

example: For these UBERON ids multiple references exist:

UBERON_0001159

If this message is shown it is neccessary to go look at /UMAP/UBERON_0001159_*.png and decide Then either:

  • delete in $DECONV_REF the three references that belong to the reference we do not want the reference from and include UBERON_id_scxa_accession in config.yaml file under "exclude_tissues_from_accessions:" OR
  • decide which reference to delete, add them to config.yaml and reurn whole generation of deconvolution reference library

Output

The output of this pipeline are :

  • deconvolution reference lib with three files per scxa accession + organism part (CO_scaled, C1 and phenData)
  • one summary file of all the references created
  • one png file per scxa accession + organism part with two UMAP plots (old + new cell type labels) for quality control

Contributions

The following scripts are taken from the CATD_snakemake pipeline which benchmarks deconvolution methods:

  • scaleTable.R
  • genRef_1.R