I have the raw basecall files from a Novaseq run that was run using the XP workflow. In each of the lanes I have 8 samples with UDI only and 8 samples with xGen UMI-UDI. I need to demultiplex the samples and generate fastq files. The command I am trying to use is
/root/bin/bcl2fastq --input-dir /pathtoNovaseqRun/Data/Intensities/BaseCalls \
--runfolder-dir /pathtoNovaseqRun/ \
--output-dir /pathto/output/files \
--sample-sheet /pathtoNovaseqRun/sample_sheet.csv \
--stats-dir /pathtoNovaseqRun/Stats \
--reports-dir /pathtoNovaseqRun/Reports \
--use-bases-mask Y51,I8Y9,I8,Y51 \
--mask-short-adapter-reads 0 \
--create-fastq-for-index-reads \
--ignore-missing-bcl \
--no-lane-splitting
This gives me the following error
ERROR: bcl2fastq::common::Exception: 2020-Sep-23 21:29:20: Success (0): /root/bin/bcl2fastq/src/cxx/lib/layout/Layout.cpp(419): Throw in function void bcl2fastq::layout::validateIndexLengths(const ReadMetadataContainer&, const std::vector<long unsigned int>&, bcl2fastq::layout::LaneInfo&)
Dynamic exception type: boost::exception_detail::clone_impl<bcl2fastq::common::InputDataError>
std::exception::what: Barcode lengths in the sample sheet do not match those in --use-bases-mask
A small excerpt from the samplesheet is linked
How can I demultiplex this set of data?
Thank you!!
You have to use a specific method for IDT xGen UDI-UMI data demultiplexing. It is described in this tech note. You can create a samplesheet for the UDI only samples and demultiplex them separately.
Thank you. So, to clarify, I will need to have separate sample sheets for the samples with UDI only and for those with the xGen UDI-UMI and then process them separately.
For the UDI only samples, can I use the code originally mentioned with the exception of the --use-bases-mask changed to Y51,I8,I8,Y51
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