bcl-convert demux of flowcell with mixed index lengths

Question

[mknulst]

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?

Answer 1

[GenoMax]

Try

Y151;I8n2;I8n2;Y151

[Istvan Albert]

Another way to say it, is that it seems that your OverrideCycles setting is incorrect, it specifies 6 reads but you only have 4, You seem to have extra ; symbols in the wrong places. the 10 cycles would be I8N2

[mknulst]

Ah now I see! Thank you both very much!