Entering edit mode
3.2 years ago
colindaven
7.0k
Dear all,
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.
https://support.illumina.com/bulletins/2020/10/upgrading-from-bcl2fastq-to-bcl-convert.html
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 ?
You should contact Illumina tech support (techsupport at illumina dot com) for an official answer on this and then come back and update the thread. BTW: Why do you think you simply had reads failing filter and not a bigger issue with the run (hardware/software)? Did you have techsupport look at this run remotely?