BCLConvert4.0_demultiplexing fastq with i5 index barcodes less than hamming distance of 3

Question

[rajeefa]

Hi ,

I have cbcl files which i want to demultiplex to fastq files using BCLConvert v4.0.3. Since i have i5 index adapters with less than 3 bases difference by default when I try to demultiplex I lose those reads with such i5 indexes. I would like to know if anyone was able to solve this barcode collision and lower the mismatch tolerance less than 3 bases by using the BarcodeMismatchIndex1 and BarcodeMismatchIndex2 as Illumina's recommendations here which I could not solve.

Answer 1

[GenoMax]

This bcl-convert version requires barcodes to differ by at least three bases so you can't do what you are asking for with it. You could simply collect all reads in "Undetermined" pool and then try your luck with a different application such as deML (LINK) or demuxbyname.sh from BBTools.

[rajeefa]

Thankyou for the answer.