sc_detect_bc {scPipe} | R Documentation

## 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, shoule 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)

[Package scPipe version 1.9.4 Index]