pycircdb overview

pycircdb is a command-line tool for annotating circRNAs using publicly available databases. Whilst it is designed to be incorporated into larger pipelines after performing circRNA quantification, pycircdb can also be used as a post-hoc tool to query circRNAs.

Note

pycircdb does not perform circRNA quantification - it just annotates the results from quantification tools.

A stable internet connection is required to download database files however, once downloaded, pycircdb will use the cached files for subsequent runs.

User Guide:

• Quick Start
  • Install pycircdb
  • Running on example data
• Invocation
  • pycircdb Options
• Configuration
  • Global Parameters
  • Sample Parameters
  • Example Configuration File
• Inputs
  • circRNA Formats
  • Quantification Tool Cheatsheet
• Outputs
  • Annotation
  • FASTA
  • miRNA
  • RBP