fastq-multx - Skipped because of distance < 2?

[Luisa B.]

Hi,

I'm using fastq-multx for the demultiplexing of my RAD-seq data.

I'm using it on several .fastq files, but for some of them this sentence appears on the terminal: "Skipped because of distance < 2" followed by a number (I guess it's the number of reads that were skipped). The demultiplexing seems to work anyway.

What does this distance < 2 refers to? Is it a problem in the reads or in the barcodes?

Thank you very much in advance for your help!

Best,

Luisa

[Erik Aronesty]

The problem is in the barcodes.   There is too much distance between the two best possible barcode choices for a given read.

[Luisa B.]

Hi and thank you for your reply.

It's not clear to me however what you mean: do you mean that the two best possible barcodes are too similar to each other (difference less than 2 nucleotides) and the program cannot be sure which one is the correct one? If this is what you mean, these reads are skipped because they cannot be assigned with certainty to a specific individuals and they end up in the file with unmatched reads. Am I correct?

Thanks again.

Luisa

[Erik Aronesty]

Yes that is 100% correct.