genetic_demux/freemuxlet

Description

Freemuxlet is a software tool to deconvolute sample identity and identify multiplets when
multiple samples are pooled by barcoded single cell sequencing. If external genotyping
data is not available, the genotyping-free version demuxlet, freemuxlet, would be recommended.

Type

r_script

Contributors

Launch

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
nsample: [ 2 ]  
verbose: [ 100 ]  
doublet_prior: [ 0.5 ]  
geno_error: [ 0.1 ]  
bf_thres: [ 5.41 ]  
frac_init_clust: [ 1 ]  
iter_init: [ 10 ]  
seed: [ 0 ]  
cap_bq: [ 20 ]  
min_bq: [ 13 ]  
min_total: [ 0 ]  
min_umi: [ 0 ]  
min_snp: [ 0 ]  
output: "$id.$key.output.freemux"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \  
  -revision 1.0.4 \  
  -main-script target/nextflow/genetic_demux/freemuxlet/main.nf \  
  -params-file params.yaml

Input

Name	Type & Properties	Description
--plp	string	Prefix of input files generated by dsc-pileup
--init_cluster	file	Input file containing the initial cluster information.
--nsample	integer	Number of samples multiplexed together
--aux_files	boolean_true	Turn on writing auxilary output files
--verbose	integer	Turn on verbose mode with specific verbosity threshold. 0: fully verbose, 100 : no verbose messages.
--doublet_prior	double	Prior of doublet.
--geno_error	double	Genotype error parameter per cluster.
--bf_thres	double	Bayes Factor Threshold used in the initial clustering.
--frac_init_clust	double	Fraction of droplets to be clustered in the very first round of initial clustering procedure.
--iter_init	integer	Iteration for initial cluster assignment (set to zero to skip the iterations).
--keep_init_missing	boolean_true	Keep missing cluster assignment as missing in the initial iteration.
--randomize_singlet_score	boolean_true	Randomize the singlet scores to test its effect.
--seed	integer	Seed for random number (use clocks if not set).
--cap_bq	integer	Maximum base quality (higher BQ will be capped).
--min_bq	integer	Minimum base quality to consider (lower BQ will be skipped).
--group_list	string	List of tag readgroup/cell barcode to consider in this run. All other barcodes will be ignored. This is useful for parallelized run.
--min_total	integer	Minimum number of total reads for a droplet/cell to be considered.
--min_umi	integer	Minimum number of UMIs for a droplet/cell to be considered.
--min_snp	integer	Minimum number of SNPs with coverage for a droplet/cell to be considered.

Name

Type & Properties

--plp

string

--init_cluster

file

--nsample

integer

--aux_files

boolean_true

--verbose

integer

--doublet_prior

double

--geno_error

double

--bf_thres

double

--frac_init_clust

double

--iter_init

integer

--keep_init_missing

boolean_true

--randomize_singlet_score

boolean_true

--seed

integer

--cap_bq

integer

--min_bq

integer

--group_list

string

--min_total

integer

--min_umi

integer

--min_snp

integer

Output

Name	Type & Properties	Description
--output -o	file output	Output directory
--out	string	freemuxlet Output file prefix

Name

Type & Properties

--output

-o

file

output

--out

string