Troubleshooting BCLConvert showing Read 1 Cycles 0 and QC Status Failed

When Read 1 cycles are reported as 0 after a BCL Convert analysis, the QC Status of the generated FASTQ file lists as QC Failed. This prevents users from using the FASTQ files as input for apps on BaseSpace.

One reason for seeing this is all R1 cycles are set as a UMI in the Sample sheet. By default, BCL Convert trims UMIs. Therefore, if all cycles are listed as UMIs, all cycles are trimmed and R1 reports as having zero cycles. To mitigate this, ensure that sample sheet also contains the setting TrimUMI, 0 to prevent BCL Convert from trimming the UMI cycles from R1. Below is an example where all of R1 is a UMI for an Illumina Single Cell 3' RNA Prep sequencing run and with the TrimUMI,0 setting.

BaseSpace Run Planning automatically adds these settings when planning a Single Cell 3' RNA Prep run. However, if manual modifications to the sample sheet for this run are required, make sure that the TrimUMI, 0 is retained in the updated sample sheet to for fastq generation and compatibility with downstream analysis options.

For any feedback or questions regarding this article (Illumina Knowledge Article #9654), contact Illumina Technical Support [email protected].