bcl-convert demux of flowcell with mixed index lengths
Hi!
I am trying to use bcl-convert to demultiplex a flowcell where samples with mixed index lengths were present. The sequencer was run with the read structure 150-10-10-150 and we generated separate samplesheets for the case where samples had 10 b long indexes and 8 b respectively.
Running bcl-convert for the specified read structure worked, but when we tried to demux the 8 b long indexes it threw an error because there was a mismatch between the index in the samplesheet and what was specified in RunInfo.xml.
The error message suggested the workaround would be to use OverrideCycles in BCLConvert_Settings to specify the deviant read structure and trim bases from cycles where supposedly there should be nothing.
I specified it like this:
OverrideCycles = Y151;I8;N2;I8;N2;Y151
Now I get a different error:
The number of reads specified in OverrideCycles must match the number of reads in the RunInfo.xml
This is the excerpt from my RunInfo.xml:
<Reads>
<Read Number="1" NumCycles="151" IsIndexedRead="N"/>
<Read Number="2" NumCycles="10" IsIndexedRead="Y"/>
<Read Number="3" NumCycles="10" IsIndexedRead="Y"/>
<Read Number="4" NumCycles="151" IsIndexedRead="N"/>
</Reads>
Does anyone know what I am doing wrong?
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