Configuration file for DSP WTA

Question

[Petesview]

Hi,

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!

[GenoMax]

data starting from Fastq

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.