chapmanb/bcbb — Issue #46: Trailing Illumina 'A' and demultiplexing
Author: b97pla
Created: 2011-11-22 14:05:08+00:00
State: open

Hi Brad,

We are seeing some issues with unexpectedly many reads ending up in the 'unmatched' category after demultiplexing. After digging around a little, we think that this may be related to the trailing 'A' that the Illumina machines add after the barcode.

More specifically, we allow one mismatch and no indels for the demuxing. It seems that the reads that are unexpectedly classified as unmatched have one mismatch in the actual 6-nucleotide barcode and are, in addition, having the trailing 'A' nucleotide miscalled.

Reading the code, it does indeed seem that for Illumina reads, the last 7 nucleotides, including the trailing 'A', of each read are matched when demultiplexing. Can you confirm that this is the case?

Our preference is to match just the 6-mer index sequence, excluding the last nucleotide in the read and it would be nice to have this done by default for Illumina reads, or at least be able to influence this behavior with a configuration option. What do you think?

Thanks
/Pontus