souporcell is a method for clustering mixed-genotype scRNAseq experiments by individual.
meta
:map
Groovy Map containing sample information e.g. [ id:'sample1' ]
[ id:'sample1' ]
bam
:file
A BAM file from cellranger containing single-cell RNA-seq alignments.
*.bam
barcodes
A barcode or whitelist TSV file from cellranger identifying individual cell barcodes.
*.tsv
clusters
:integer
Number of clusters.
meta2
fasta
A reference fasta file.
*.fasta
*/clusters.tsv
TSV file listing cell barcodes with singlet/doublet status, assigned cluster, and per-cluster log-loss metrics
clusters.tsv
vcf
*/cluster_genotypes.vcf
A vcf with genotypes for each cluster for each variant in the input vcf from freebayes.
cluster_genotypes.vcf
ambient_rna
*/ambient_rna.txt
Contains the ambient RNA percentage detected
ambient_rna.txt
versions
versions.yml
File containing software versions
Clustering scRNAseq by genotypes.
