I have a specific requirement that involves adapting match_cell_barcode function to accommodate different barcode and UMI lengths. Currently, the software assumes a standard barcode length of 16 and a UMI length of 10, based on 10X kit.
I would like to request if it would be possible to modify these parameters according to my needs, since I’m using a custom single-cell ONT library with same flanking sequence (CTACACGACGCTCTTCCGATCT) but barcode length of 11 and UMI of 14 bp respectively.
Regarding the UMI length, it can be specified by command line.
I would like to ask you a feedback:
I modified the source code of match_cell_barcode by substituting all ’16’ occurrences with ’11’.
For the UMI I specified by command line my length (14).
Edit distance allowed : 2 (considering that I have a minimum hamming distance of 3 between my custom barcodes).
Are these modifications correct and sufficient in order to have a proper barcode and UMI assignment, or do I have to change something else in the source code of match_cell_barcode?
Sorry in advance but I’m not an expert in c++.
Best
Hi,
Thanks for developing FLAMES.
I have a specific requirement that involves adapting match_cell_barcode function to accommodate different barcode and UMI lengths. Currently, the software assumes a standard barcode length of 16 and a UMI length of 10, based on 10X kit. I would like to request if it would be possible to modify these parameters according to my needs, since I’m using a custom single-cell ONT library with same flanking sequence (CTACACGACGCTCTTCCGATCT) but barcode length of 11 and UMI of 14 bp respectively.
Regarding the UMI length, it can be specified by command line. I would like to ask you a feedback:
Are these modifications correct and sufficient in order to have a proper barcode and UMI assignment, or do I have to change something else in the source code of match_cell_barcode?
Sorry in advance but I’m not an expert in c++. Best