Barcode Discovery - GenomicsCoreLeuven/GBSX GitHub Wiki
This program searches for possible barcodes and barcode enzyme combinations.
Designed for the discovery of sequencing errors, or unused barcodes when a large
proportion of the demultiplex is undetermined.
Mandatory parameters:
-f1
the name of the input file (mandatory)
Optional parameters:-min
the minimum length of the barcode (standard 6)-max
the maximum length of the barcode (standard 10)-gzip
use gzip files as input and output (standard false)-o
the output directory (standard the directory of execution)-ea
Add enzymes from the given file (keeps the standard enzymes, and add the new) (enzyme file: no header, enzyme name tab cutsites (multiple cutsites are comma separeted)) (example: enzyme ApeKI and restriction site G^CWGC: "ApeKI \tab CAGC,CTGC") (only use once, not use -er)-er
Replace enzymes from the given file (do not keep the standard enzymes) (enzyme file: no header, enzyme name tab cutsites (multiple cutsites are comma separeted)) (example: enzyme ApeKI and restriction site G^CWGC: "ApeKI \tab CAGC,CTGC") (only use once, not use -ea)-barmin
The minimum occurance of a barcode before it is shown in the results (standard: 200)-barmax
The maximum occurance of barcodes shown in the output (increasing this number will increase ram usage, but gives a slightly better result) (standard: 100)-barmis
The percentage of mismatches that may occure between barcodes (integer between 1 and 10) (standard: 10)