Welcome to GEMmaker’s documentation!¶
GEMmaker is a Nextflow workflow for large-scale gene expression sample processing, expression-level quantification and Gene Expression Matrix (GEM) construction. Results from GEMmaker are useful for differential gene expression (DGE) and gene co-expression network (GCN) analyses. The GEMmaker workflow currently supports Illumina RNA-seq datasets.
GEMmaker is an nf-core compatible workflow, however, GEMmaker is not an official nf-core workflow. This is because nf-core offers the nf-core/rnaseq workflow which is an excellent workflow for RNA-seq analysis that provides similar functionality to GEMmaker. However, GEMmaker is different in that it can scale to thousands of samples without exceeding local storage resources by running samples in batches and removing intermediate files. It can do the same for smaller sample sets on machines with less computational resources. This ability to scale is a unique adaption that is currently not provided by Nextflow. When Nextflow does provide support for batching and scaling, the nf-core/rnaseq will be updated and GEMmaker will probably be retired in favor of the nf-core workflow. Until then, if you are limited by storage GEMmaker can help!
Development of GEMmaker was funded by the U.S. National Science Foundation Award #1659300.
- Test GEMmaker
- Step 1: Prepare Genome Data
- Step 2: Prepare Sample Data
- Step 3: Run GEMmaker
- Step 4: View Output and Results
- What to do with the GEM?
- WARNING about “sticked on revision”
- ERROR : Unknown image format/type
- ERROR : No valid /bin/sh in container
- ERROR : Failed to set loop flags on loop device: Resource temporarily unavailable
- Exception in thread “main” java.lang.OutOfMemoryError: Java heap space
- Why is it taking so long to pull a docker/singularity image?
- GEMmaker seems hung and does not complete
- SLURM: exceeded memory limit
- Error: terminated with an error exit status (127)
- Get Help or Suggest Improvements
- Citing GEMmaker
- Publiations Citing GEMmaker