Geomxngspipeline
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Description
The GeoMx NGS Pipeline, developed by NanoString, is an essential part of the GeoMx NGS workflow. The Pipeline processes RNA-sequencing files (FASTQ files) from Illumina sequencers according to parameters defined in the Configuration File (which is generated from the GeoMx DSP run). The Pipeline processes information from these files and outputs .dcc files, which can then be uploaded to the GeoMx DSP system for data analysis.
Environment Modules
Run module spider geomxngspipeline to find out what environment modules are available for this application.
System Variables
- HPC_GEOMXNGSPIPELINE_DIR - installation directory
- HPC_GEOMXNGSPIPELINE_BIN - executable directory
Additional Information
- The pipeline must be run in an interactive session because of an interactive prompt for correcting the number of threads for the available computational resources.
- Be sure to set the following environment variable "export DOTNET_SYSTEM_GLOBALIZATION_INVARIANT=1" prior to executing the pipeline.