Code repository related to preprint.

Multimodal chromatin profiling using nanobody-based single-cell CUT&Tag Marek Bartosovic, Gonçalo Castelo-Branco bioRxiv 2022.03.08.483459; doi: https://doi.org/10.1101/2022.03.08.483459

Processed files - Seurat objects, fragments file (cellranger), bigwig tracks per cluster and .h5 matrices are available as supplementary files in the GEO repository https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE198467

conda env create -f env/environment.yaml

R
install.packages(c('argparse','ggplot2','funr','Signac','scales','Seurat','rmarkdown','mclust','GGally','BiocManager','patchwork','markdown','UpSetR','pheatmap','viridis','purrr','Rmagic','devtools','raster'))
BiocManager::install(c('ensembldb','EnsDb.Mmusculus.v79','GenomeInfoDb', 'GenomicRanges', 'IRanges', 'Rsamtools','BiocGenerics','rtracklayer','limma','slingshot','BiocGenerics', 'DelayedArray', 'DelayedMatrixStats','limma', 'S4Vectors', 'SingleCellExperiment','SummarizedExperiment', 'batchelor', 'Matrix.utils')))

https://github.com/lh3/seqtk

python3 -m pip install papermill

use fasterq-dump or alternative to download the fastq files

https://github.com/ncbi/sra-tools/wiki/HowTo:-fasterq-dump

GEO repository

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE198467

git clone https://github.com/mardzix/bcd_nano_CUTnTag

Change config/config.yaml and specify path to

1. Absolute path to fastq files
2. Specific path to the tmp folder (Create any folder, e.g. in home)
3. Specify conda environment to use
4. Modify path to cellranger reference

Pipeline is implemented in workflow management software Snakemake

Change the cluster-specific profile to your preference (e.g. slurm, condor etc.), or run without profile

For some example profiles see:

• https://snakemake.readthedocs.io/en/stable/executing/cli.html#profiles

• https://github.com/Snakemake-Profiles/slurm

• https://github.com/Snakemake-Profiles/htcondor

snakemake --snakefile code/workflow/Snakefile_single_modality.smk  --cores 16 --profile htcondor -p                                                                              

Johannes Köster, Sven Rahmann, Snakemake—a scalable bioinformatics workflow engine, Bioinformatics, Volume 28, Issue 19, 1 October 2012, Pages 2520–2522, https://doi.org/10.1093/bioinformatics/bts480