bc_splitVDJ: Parse VDJ recombination (experimental)

In wenjie1991/CellBarcode: Cellular DNA Barcode Analysis toolkit

Parse VDJ recombination (experimental)

Description

Script to split barcodes from the genetic 'barcode mouse' construct as generated in the lab of Ton Schumacher (NKI, NL) in its remaining constant V, D and J elements and the modified elements (additions/deletions) in between those constant parts.

Usage

bc_splitVDJ(
  seqs,
  v_part = "TCCAGTAG",
  d_fwd = "TCTACTATCGTTACGAC",
  d_inv = "GTCGTAACGATAGTAGA",
  j_part = "GTAGCTACTACCG"
)

Arguments

seqs	a character vector contains the barcode sequences.
v_part	a string given the V part sequence.
d_fwd	a string given the D region forwrad sequence.
d_inv	a string given the D region inverted sequence.
j_part	a string given the J region sequence.

Value

A list contains two data.frame named add.del.ok and add.del.err, which contain columns with the remaining constant parts and inserted/deleted parts

Examples

## prepare input sequence
seq_v <- c(
    "TCCAGTAGCTACTATCGTTACGAGTAGCTACTACCG",
    "TCCAGTAGCTACTATCGTTACGACGTAGCTACTACCG",
    "TCCATACTATCGTTACGACGTAGCTACTACG",
    "TCCAGTAGTCGTAACGATAGTAGAGTAGCTACTACCG"
    )

## split the sequences
bc_splitVDJ(seq_v)

wenjie1991/CellBarcode documentation built on Aug. 10, 2024, 11:02 a.m.