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')))
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
- Absolute path to fastq files
- Specific path to the tmp folder (Create any folder, e.g. in home)
- Specify conda environment to use
- 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:
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