sc_gene_counting: sc_gene_counting
In scPipe: pipeline for single cell RNA-seq data analysis

Description Usage Arguments Value Examples

Generate gene counts matrix with UMI deduplication

1	sc_gene_counting(outdir, bc_anno, UMI_cor = 2, gene_fl = FALSE)

`outdir`	output folder containing `sc_demultiplex` output
`bc_anno`	barcode annotation comma-separated-values, first column is cell id, second column is cell barcode sequence
`UMI_cor`	correct UMI sequencing error: 0 means no correction, 1 means simple correction and merge UMI with distance 1. 2 means merge on both UMI alignment position match.
`gene_fl`	whether to remove low abundance genes. A gene is considered to have low abundance if only one copy of one UMI is associated with it.

no return

data_dir="celseq2_demo"
barcode_annotation_fn = system.file("extdata", "barcode_anno.csv",
package = "scPipe")
## Not run: 
# refer to the vignettes for the complete workflow
...
sc_gene_counting(data_dir, barcode_annotation_fn)
...

## End(Not run)