riboWaltz

note

Computes P-site offsets and performs quality control for ribosome profiling data.

https://github.com/LabTranslationalArchitectomics/riboWaltz

riboWaltz computes P-site offsets and performs quality control for ribosome profiling data.

The module parses QC output files from riboWaltz and generates visualizations for:

• P-site region distribution: Shows where P-sites map across transcript regions (5' UTR, CDS, 3' UTR). Good Ribo-seq data shows >70% CDS enrichment.
• Reading frame distribution: Shows P-site distribution across reading frames for each transcript region. Frame 0 should be >50% in CDS but not in UTRs.
• Metaprofiles: Shows P-site frequency around start and stop codons. Good data shows trinucleotide periodicity with Frame 0 peaks.

Supported input files:

• *ribowaltz*psite_region.tsv - P-site region distribution
• *ribowaltz*frames.tsv - Reading frame distribution
• *ribowaltz*metaprofile_psite.tsv - Metaprofile around start/stop codons

Files must contain "ribowaltz" in the filename since headers are generic. Both tab-delimited and comma-delimited files are supported.

File search patterns

ribowaltz/frames:
  contents_re: "sample[,\t]region[,\t]frame[,\t]count[,\t]scaled_count"
  fn: '*ribowaltz*frames.tsv'
  num_lines: 1
ribowaltz/metaprofile:
  contents_re: "sample[,\t]region[,\t]x[,\t]y"
  fn: '*ribowaltz*metaprofile_psite.tsv'
  num_lines: 1
ribowaltz/psite_region:
  contents_re: "sample[,\t]region[,\t]count[,\t]scaled_count"
  fn: '*ribowaltz*psite_region.tsv'
  num_lines: 1