Shoji

Shoji is a toolset for the analysis of eCLIP/iCLIP datasets, designed to be a flexible replacement for htseq-clip package. This python package can be used to generate files necessary for data analysis using the companion R/Bioconductor package DEWSeq

Shoji data flow

Differences to htseq-clip

• Flag --splitExons is removed, Shoji cannot split exons into components

• Flag --split-intron is added. If an intron overlaps exon from another gene, using this tag will split the intron into non overlapping chunks

• Piping output disabled. Output file names MUST be specified

• count function writes output files in Apache parquet file format

Contents:

• overview
  • Annotation
  • Extraction
  • Counting
  • Further analysis
• installation
  • dependencies
  • installation
• documentation
  • Annotation
  • Extraction
  • Counting
  • Helpers

Hentze lab, EMBL Heidelberg