sc_detect_bc: sc_detect_bc

In LuyiTian/scPipe: Pipeline for single cell multi-omic data pre-processing

sc_detect_bc

Description

Detect cell barcode and generate the barcode annotation

Usage

sc_detect_bc(
  infq,
  outcsv,
  prefix = "CELL_",
  bc_len,
  max_reads = 1e+06,
  min_count = 10,
  number_of_cells = 10000,
  max_mismatch = 1,
  white_list_file = NULL
)

Arguments

infq	input fastq file, should be the output file of sc_trim_barcode
outcsv	output barcode annotation
prefix	the prefix 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.
number_of_cells	number of cells kept in result. (default: 10000)
max_mismatch	the maximum mismatch allowed. Barcodes within this number will be considered as sequence error and merged. (default: 1)
white_list_file	a file that list all the possible barcodes each row is a barcode sequence. the list for 10x can be found at: https://community.10xgenomics.com/t5/Data-Sharing/List-of-valid-cellular-barcodes/td-p/527 (default: NULL)

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)

LuyiTian/scPipe documentation built on Dec. 11, 2023, 8:21 p.m.