I am currently re-processing Digital Spatial Profiling (Whole Transcriptome Atlas) data starting from Fastq. In order to run GeoMx NGS pipeline to convert this into DCC format, I need a configuration file in the ini format. I was wondering whether each specific experiment comes with its unique ini configuration, or whether there is a general configuration for whole transcriptome atlas which I can download. I noticed that the pkc configuration can be downloaded from the Nanstrong official website here. But I'm not sure whether this pkc configuration is what the pipeline requires as input. Thanks for the help!
Generally did this with the entire flowcell folder and not fastq files. The data needs to be demultiplexed in a way that the fastq files are named with DSP* sample names that are in the samplesheet for the experiment.
I need a configuration file in the ini format. I was wondering whether each specific experiment comes with its unique ini configuration
Never looked inside these files but an experiment specific samplesheet (for demultiplexing) and the .ini file were provided in a .zip readout package for each GeoMX run. The samplesheet was needed to run the demultiplexing since it had the DSP* names for the samples that end up on the fastq files.
The configuration file required by the GeoMx NGS Pipeline is a .ini file containing pipeline processing parameters, and it is unique to each readout group (i.e., experiment-specific). This file is generated automatically by the GeoMx DSP instrument and included in the zipped readout package that you download after finalising your collection plate(s). It is not a general file that can be downloaded separately for the Whole Transcriptome Atlas; instead, you will need the one from your original experiment's readout package to process the FASTQs into DCC format.
The PKC configuration files available on the NanoString website are separate—they provide assay-specific details like target-to-barcode associations for RNA or protein panels (e.g., Human_WTA_v1.0)—and are not the input required by the NGS Pipeline itself. If you no longer have access to your original readout package (which also includes the samplesheet for demultiplexing), I recommend contacting NanoString support at spatial.support@nanostring.com to regenerate it.
