Some methods developed place a barcode-like sequence at the beginning of an R1 sequence file, while others default to not generating index reads.
Could make one flag that demultiplexes through read names, as there may not be any index files generated. dualDemultiplexR would need to split the barcode sequences from the read names of R1 and R2 files. Not a hard problem to solve with stringr.
Alternatively, add someway to redirect barcode parsing to read (R1 or R2) sequences.
Further, should be able to make dualDemultiplexR work with a single barcode for added function.
Some methods developed place a barcode-like sequence at the beginning of an R1 sequence file, while others default to not generating index reads.
Could make one flag that demultiplexes through read names, as there may not be any index files generated. dualDemultiplexR would need to split the barcode sequences from the read names of R1 and R2 files. Not a hard problem to solve with stringr.
Alternatively, add someway to redirect barcode parsing to read (R1 or R2) sequences.
Further, should be able to make dualDemultiplexR work with a single barcode for added function.