GenomeComb

sc_demultiplex

Format

cg sc_demultiplex sampledir dmfile refseq

Summary

demultiplexes ont single cell results into separate samples based on a demultiplexing file

Description

cg sc_demultiplex takes as arguments a sample directory and a demultiplexing file.

The source is a normal sample directory produced by scywalker analysis of ont single cell data.

The demultiplexing file is a tsv file with (at least) the fields cell and sample, in which each line assigns a cell to a sample. (If these fields are not present, alternatives are accepted: barcode or cellbarcode for cell; donor_id or subsample for sample

Foreach sample in the demultiplexing file, a new sample is created next to the original sample, named dm_<dmsamplename><sample> where <sample> is the original sample name, and <dmsamplename> is the name for the "new" sample given in the demultiplexing file In these all important analysis files are recreated containing only the cells assigned to the dmsample. The original pooled sample is not removed, as it has information not in the demultiplexed samples (unassigned cells, reads not assigned to cells, ...)

Arguments

sampledir
original (pooled) sample directory (result fo scywalker analysis)
dmfile
tsv file assigning cells to (new/demultiplexed) samples
refseq
genome reference sequence, needed for (oa) making crams

Category

Singlecell