Welcome to the QBiC analysis documentation!

This documentation contains the guidelines for running Bioinformatics analyses at QBiC. How to run nf-core pipelines, which are the latest tested releases and how to report the results.

You can contribute or add changes to the documentation, by making a pull request to the pipelines-docs github repository.

Additionally, this repository will collect example reports and analysis scripts that are necessary for the different analysis types.

Contents:

• Submitting jobs to the cluster
  • Submitting Nextflow pipelines
  • Screen sessions
  • Useful scheduler commands
  • Submitting custom jobs
• RNAseq analysis
  • RNAseq pipeline
  • Differential expression analysis
  • Reporting
• Exome seq analysis
  • Input tsv file
  • Variant calling tools
  • Whole Genome Sequencing
  • Whole Exome and Targeted Sequencing
  • Reporting
• 16S amplicon sequencing
  • Ampliseq pipeline
  • Reporting
• HLA typing
  • HLAtying nf-core pipeline
  • HLA typing for type II
• Debugging
  • General error reporting
  • Common errors
• Updating igenomes

Indices and tables

• Index

• Module Index

• Search Page