Match Cell Barcodes

demultiplex reads with flexiplex

Usage

find_barcode(
  fastq,
  barcodes_file,
  max_bc_editdistance = 2,
  max_flank_editdistance = 8,
  reads_out,
  stats_out,
  threads = 1,
  pattern = c(primer = "CTACACGACGCTCTTCCGATCT", BC = paste0(rep("N", 16), collapse =
    ""), UMI = paste0(rep("N", 12), collapse = ""), polyT = paste0(rep("T", 9), collapse
    = "")),
  TSO_seq = "",
  TSO_prime = 3,
  full_length_only = FALSE
)

Arguments

fastq

input FASTQ file path

barcodes_file

path to file containing barcode allow-list, with one barcode in each line

max_bc_editdistance

max edit distances for the barcode sequence

max_flank_editdistance

max edit distances for the flanking sequences (primer and polyT)

reads_out

path of output FASTQ file

stats_out

path of output stats file

threads

number of threads to be used

pattern

named character vector defining the barcode pattern

TSO_seq

TSO sequence to be trimmed

TSO_prime

either 3 (when TSO_seq is on 3' the end) or 5 (on 5' end)

full_length_only

boolean, when TSO sequence is provided, whether reads without TSO are to be discarded

Value

invisible()

Examples

outdir <- tempfile()
dir.create(outdir)
bc_allow <- file.path(outdir, "bc_allow.tsv")
R.utils::gunzip(filename = system.file("extdata/bc_allow.tsv.gz", package = "FLAMES"), destname = bc_allow, remove = FALSE)
find_barcode(
  fastq = system.file("extdata/fastq", package = "FLAMES"),
  stats_out = file.path(outdir, "bc_stat"),
  reads_out = file.path(outdir, "demultiplexed.fq.gz"),
  barcodes_file = bc_allow
)
#> FLEXIPLEX 0.96.2
#> Setting max barcode edit distance to 2
#> Setting max flanking sequence edit distance to 8
#> Setting read IDs to be  replaced
#> Setting number of threads to 1
#> Search pattern: 
#> primer: CTACACGACGCTCTTCCGATCT
#> BC: NNNNNNNNNNNNNNNN
#> UMI: NNNNNNNNNNNN
#> polyT: TTTTTTTTT
#> Setting known barcodes from /tmp/Rtmpg58CKQ/file1a582d205cc5/bc_allow.tsv
#> Number of known barcodes: 143
#> Searching for barcodes...
#> Number of reads processed: 393
#> Number of reads where a barcode was found: 368
#> Number of reads where more than one barcode was found: 4
#> All done!
#> Skipping TSO trimming...