ChimPipe Documentation

ChimPipe is a computational method for the detection of novel transcription-induced chimeric transcripts and fusion genes from Illumina Paired-End RNA-seq data. It combines junction spanning and paired-end read information to accurately detect chimeric splice junctions at base-pair resolution.

ChimPipe source code is freely available in our GitHub repository.

Table of contents:

• Installation
  • Download
  • Requirements
• Manual
  • Input
  • Execute ChimPipe
  • Output
• Tutorial
  • 1. Download ChimPipe
  • 2. Download all-in-one package
  • 3. Execute ChimPipe on MCF-7
  • 4. Examine your output
• FAQ
  • Quality offset encoding
  • RNA-seq protocols accepted
  • Read identifier format
• Downloads
  • GEM genome indices
  • GEM transcriptome indices
  • Similarity between gene pair matrices
• Contact

License

ChimPipe is distributed under the GPLv3.