sc_detect_bc {scPipe}R Documentation

sc_detect_bc

Description

Detect cell barcode and generate the barcode annotation

Usage

sc_detect_bc(infq, outcsv, suffix = "CELL_", bc_len, max_reads = 1e+06,
  min_count = 10, max_mismatch = 1)

Arguments

infq

input fastq file, shoule be the output file of sc_trim_barcode

outcsv

output barcode annotation

suffix

the suffix of cell name (default: 'CELL_')

bc_len

the length of cell barcode, should be consistent with bl1+bl2 in sc_trim_barcode

max_reads

the maximum of reads processed (default: 1,000,000)

min_count

minimum counts to keep, barcode will be discarded if it has lower count. Default value is 10. This should be set according to max_reads.

max_mismatch

the maximum mismatch allowed. Barcodes within this number will be considered as sequence error and merged. (default: 1)

Value

no return

Examples

## Not run: 
# `sc_detect_bc`` should run before `sc_demultiplex` for
# Drop-seq or 10X protocols
sc_detect_bc("input.fastq","output.cell_index.csv",bc_len=8)
sc_demultiplex(...,"output.cell_index.csv")

## End(Not run)



[Package scPipe version 1.2.1 Index]