To run scmulti:
python run.py -o results_dir \
--rna scrna.anno.h5ad \
--rds scrna.anno.rds \
--atac atac.anno.h5ad \
--name projectA \
--fragment fragments.tsv.gz \
--meta Metadata.tsv \
--gtf species_gene_annotation.gtf \
--fasta reference_genome.fa \
--chromsize sizes.genome \
--upstream 0 1500 \
--downstream 100 15000
To make a cisTarget database for species other than human or mouse:
python custom_databases.py --prefix speciesX
--fasta reference.fasta
--output /path/to/save/
--consensus_regions consensus_regions.bed
--ortholog human_speciesX_ortholog.tsv
--ref_species hg
--atac atac.h5ad
--bedpath /path/to/bedtools
To run label transfer:
Rscript label_transfer.R --rna scrna.anno.rds \
--atac integrated.atac.rds \
-m Metadata.tsv \
--fragments fragments.tsv.gz \
--gff species_gene_annotation.gtf \
--name projectA \
-o results_dir/
To integrate multiple ATAC datasets (by different libraries):
Rscript integrate.R -n name --list datasets_ids.txt --data_path /path/to/samples/
Example of a datasets_ids.txt:
sample_id_1
sample_id_2
sample_id_3
...
Example of a data path:
|--/path/to/samples/
|--sample_id_1
|--Peak_matrix
|--barcodes.tsv
|--matrix.mtx
|--peak.bed
|--sample_id_2
|--Peak_matrix
|--barcodes.tsv
|--matrix.mtx
|--peak.bed