The DRAGEN Protein Quantification application is designed to perform counting and normalization for proteomics data from the Illumina Protein Prep pipeline. It converts data from the binary base call (BCL) files, generated by Illumina NovaSeq 6000 or NovaSeq X Series systems, into the normalized proteomic counts. Upon completion of sequencing, the application is automatically initiated for analysis on BaseSpace Sequence Hub (BSSH) or Illumina Connected Analytics (ICA).
The sections below exemplify how to configure the instrument(s) for autolaunching the secondary analysis, manually initiate an analysis, and requeue an analysis.
On your instrument, log into your workgroup and select the following run setup options:
Workflow: NovaSeq Standard
Read length: 15, 10, 10, 0
[NovaSeq 6000] Upload the v2 sample sheet generated by the BSSH Run Planner tool to the sequencing instrument.
[NovaSeq X Series] No action is required. The v2 sample sheet automatically displays on the instrument as a planned run.
Select the appropriate Illumina Protein Prep custom recipe for your sequencing instrument and flowcell. During the run, data is uploaded automatically to BSSH. Primary analysis and secondary analysis are completed automatically through autolaunch.
[Optional] Use the BaseSpace Sequence Hub to monitor the run from start to completion.
For additional information on autolaunch, refer to the Cloud Analysis Auto-launch page.
If manual mode sequencing is performed, or autolaunch is unsuccessful, there is an option to manually upload a completed run folder to BSSH and kick off the autolaunch analysis. To use this method, the samplesheet must be in the uploaded run folder, and be named "SampleSheet.csv".
Follow the instructions from the BSSH CLI documentation for manually uploading the run folder to BSSH.
Follow the instructions described in Requeue Analysis Page (Requeue Analysis in BaseSpace tab).
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