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

Description Usage Arguments Value Examples

Detect cell barcode and generate the barcode annotation

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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)

`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)

no return

## 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)