on a NextSeq550, I can get failed reads (not PF) with
--with-failed-reads using bcl2fastq.
With the more modern bclconvert software, this does not exist.
Also, it seems failed reads are not saved any more by the Novaseq, which is problematic for one poor run we had recently.
std::exception::what: Cannot specify '--with-failed-reads' with cbcl input data. Failed reads are not stored in cbcl files.
Does anyone know how to set an option to save reads (eg prior to sequencing) or if this option is not available at all on Novaseq ?