Description

souporcell is a method for clustering mixed-genotype scRNAseq experiments by individual.

Input

name:type
description
pattern

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:'sample1' ]

bam{:bash}

:file

A BAM file from cellranger containing single-cell RNA-seq alignments.

*.bam

barcodes{:bash}

:file

A barcode or whitelist TSV file from cellranger identifying individual cell barcodes.

*.tsv

clusters{:bash}

:integer

Number of clusters.

meta2{:bash}

:map

Groovy Map containing sample information e.g. [ id:'sample1' ]

fasta{:bash}

:file

A reference fasta file.

*.fasta

Output

name:type
description
pattern

clusters{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:'sample1' ]

*/clusters.tsv{:bash}

:file

TSV file listing cell barcodes with singlet/doublet status, assigned cluster, and per-cluster log-loss metrics

clusters.tsv

vcf{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:'sample1' ]

*/cluster_genotypes.vcf{:bash}

:file

A vcf with genotypes for each cluster for each variant in the input vcf from freebayes.

cluster_genotypes.vcf

ambient_rna{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:'sample1' ]

*/ambient_rna.txt{:bash}

:file

Contains the ambient RNA percentage detected

ambient_rna.txt

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

Tools

maintainers
Github user seohyonkim
Github user LuisHeinzlmeier
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