sc_detect_bc {scPipe} | R Documentation |
Detect cell barcode and generate the barcode annotation
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
|
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 |
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 |
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)