modules/ribowaltz
Calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data
Description
Calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data
Input
Map containing reference information for the reference genome GTF file
e.g. [ id:'Ensembl human v.111' ]
Map containing reference information for the reference genome FASTA file
e.g. [ id:'Ensembl human v.111' ]
Output
Text file with the extremity used for the offset correction step and the best offset for each sample (optional, in case no offsets could be determined, usually because no reads pass filtering criteria)
*.best_offset.txt TSV file containing P-site offsets for each read length (optional, in case no offsets could be determined, usually because no reads pass filtering criteria)
*.psite_offset.tsv.gz TSV file containing P-site transcriptomic coordinates and information for each alignment (optional)
*.psite.tsv.gz TSV file with codon-level RPF coverage for each transcript (optional)
*.codon_coverage_rpf.tsv.gz TSV file with codon-level P-site coverage for each transcript (optional)
*.codon_coverage_psite.tsv.gz TSV file with CDS P-site in-frame counts for each transcript (optional)
*.cds_coverage_psite.tsv.gz TSV file with CDS P-site in-frame counts for each transcript, excluding P-sites within defined distances to start and stop codons (defined by passing —exclude_start and —exclude_stop with the number of nucleotides) (optional)
*nt_coverage_psite.tsv.gz maintainer
