Splitting individual sample based on barcode

[shis]

Hello,
I have GBS sequence file with 384 samples of two different parents. Now I want to separate individual sample based barcode sequence using Fastx barcode_splitter.pl program developed by Hannon Lab. The problem is this program require same length of barcodes. But I have different length of barcode. Is there any command line to make similar length of barcode based on barcode sequences and ApekI enzyme information?

Thanks

[nucacidhunter]

Two possible approaches from a non-bioinformatician:

1- convert shorter barcodes to the the length of longest barcode by adding some bases from restriction overhangs if there will be enough edit distance among barcodes

2- run data through demulplexing pipeline several times starting with the longest barcode and running the remaining reads with the next shorter one

[shis]

Hello nucacidhunter,
Thanks for your reply. However, I would like to know your first opinion about to convert shorter barcodes into longer by adding some bases of ApekI restriction enzyme. Could you suggest any command line to do this.

Regards,
Shis

Two possible approaches from a non-bioinformatician:

1- convert shorter barcodes to the the length of longest barcode by adding some bases from restriction overhangs if there will be enough edit distance among barcodes

2- run data through demulplexing pipeline several times starting with the longest barcode and running the remaining reads with the next shorter one

[nucacidhunter]

ApeKI overhang is CWGC (W: A or T). So you can add up to four bases to extend barcode length. W would make this difficult because you will have to create two sets one with A and one with T. I would do it with Excel.