Add a "golay" barcode?

[Andor Kiss]

Hello,

  I have done some 16S & 18S emp based protocol sequencing.  I have also done some libraries where the barcode is not a GOLAY barcode.  Is there a way to ADD a 12 nt barcode to the "GOLAY" list so that I can still use the error checking function of the spilt_libraries.py script?

  Or is there a better approach that I'm not seeing.

Thanks,
Andor

[Tony Walters]

Hello Andor,

I have attached files containing all (4096) golay codes and a filtered set, from which you should be able to find unique Golay codes you can use.

 

I think it may be safer to use a filtered version of the codes, that I've also included, which removes any Golay code that has a homopolymer of 4+ nucleotides within it, or any Golay code with 3 of the same nucleotide occurring at one of the ends of the barcode.

You do want to make sure that the given codes are in the same orientation as your existing barcodes, and reverse complement them to make them match if they are not.

-Tony

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[Tony Walters]

I should note that the filtering was done when more 454 runs were being used, so the homopolymer issue may not be much of an issue. Another concern is homogenous signal, e.g. the second nucleotide is 80% A. You probably want to visually inspect the barcodes that you want to add to confirm that the bases aren't terribly unbalanced for each position.

[Andor Kiss]

Hi Tony,

   Thanks - Actually because the barcode wasn't in the dataset, and someone had already "made" the libraries, what I did was to split out the libraries with the GOLAY codes, and then re-split that data with ONLY the four wierd or non-GOLAY codes.  Seems to have worked.

Regards,
Andor

[Tony Walters]

Ah, sorry, I thought you were at the barcode creation stage-your approach is sound for dealing with the mixed barcode types.

-Tony

[Andor J Kiss]

Yeah, if I had any say in the matter, I would NOT have used the barcodes that this group choose...

anyways...