scRNA-seq and scATAC-seq datasets were produced with 10x Genomics (v3) technology and further preprocessed with Cell Ranger. Since multiple donors were mixed in the same lane, donor demultiplexing based on genotype required.
scRNA-seq
Note: Input fastq file names in the following format: sample1_S1_L001_R1_001.fastq.gz, sample1_S1_L001_R2_001.fastq.gz
module load cellranger/3.0.1
cellranger count --id=
--transcriptome=<GRCh38-3.0.0_reference>
--sample=
--fastqs=<directory containing R1,R2 fastqs>
Variant Calling for single cells using cellSNP
cellSNP v0.1.7
cellSNP -b <filtered_barcodes>
-s <possorted_bam>
-O <output_directory>
-R <region_vcf_file>
-p 22
--minMAF 0.1
--minCOUNT 100
vireo v0.1.8 vireo -c <cell_data> -N <n_donors> -o <out_dir>
scATAC-seq
Note: Input fastq file names in the following format: sample1_S1_L001_I1_001.fastq.gz sample1_S1_L001_R1_001.fastq.gz sample1_S1_L001_R2_001.fastq.gz sample1_S1_L001_R3_001.fastq.gz
module load cellranger-atac/1.2.0
cellranger-atac count --id=
--reference=<GRCh38_reference>
--fastqs=
--sample=