geomxngspipeline¶

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.

Environment Variables¶

HPC_GEOMXNGSPIPELINE_DIR - installation directory
HPC_GEOMXNGSPIPELINE_BIN - container directory

Categories¶

NGS