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sc_pseudobulk

Format

cg sc_pseudobulk scgenefile scisoformfile groupfile

Summary

make pseudobulk files of sc_gene and sc_transcript files based on an sc_group file

Description

cg sc_pseudobulk creates pseudobulk files at the gene and transcript level starting from the single cell gene and transcript files, and a grouping file that assigns each cell/barcode to a group (e.g. celltype) The resulting pseudobulk files will be named pb_gene_counts-rootname.tsv.zst pb_isoform_counts-rootname.tsv.zst where rootname is based on the filename of the given groupfile

Arguments

scgenefile

tab separated file with gene information (output of e.g. scywalker) and UMI counts per gene/per cell

scisoformfile

tab separated file with transcript information (in the transcript tsv format, output of e.g. scywalker) and UMI counts per gene/per cell

groupfile

tsv file containing assignement of cells/barcodes to cell-types (or any other grouping)

Category

RNA