NGS demultiplexing

Question

[SurdanBurasi]

Hello everyone, I am working on a linkage project for Sars COV-2. I used Illumina iseq1000 for sequencing. The indexes I use for the study are designed as 10bp, but they were entered as 8bp during the operation of the device. When I demultiplex with bcl2fastq, all data is written to the undetermined file. how can I fix this?

Answer 1

[GenoMax]

As long as the fist 8 bp were unique you can simply edit the samplesheet to shorten the indexes and then re-run the demultiplexing. If those 8 bp are not unique among samples then there is not much you can do except re-run with correct length of indexes.

There are other options such as demuxbyname.sh (from BBMap suite) and deML (LINK) that may be options to work with "undetermined" files in case you do not have the ability to re-run bcl2fastq.

[SurdanBurasi]

My index are have a unique sequence (ITD xGen Normalase UDI Primers). The only problem is that during the operation, 8 BP was entered instead of 10bp in the definition of the Device.