Accurate detection of short and long active ORFs using Ribo-seq data
meta:map
Map containing riboseq sample information e.g. `[ id:‘sample1’, single_end
bam:file
BAM/CRAM/SAM file
*.{bam,cram,sam}
bai:file
Index for sorted BAM/CRAM/SAM file
*.{bai}
meta2:map
Map containing reference information for the candidate ORFs e.g. [ id:'Ensembl human v.111' ]
[ id:'Ensembl human v.111' ]
candidate_orfs:file
TSV file with candidate ORFs from ‘ribotricer prepareorfs’
*.tsv
protocol
Groovy Map containing riboseq sample information e.g. `[ id:‘sample1’, single_end
*_protocol.txt:file
txt file containing inferred protocol if it was inferred (not supplied as input)
*_protocol.txt
bam_summary
*_bam_summary.txt:file
Text summary of reads found in the BAM
*_bam_summary.txt
read_length_dist
*_read_length_dist.pdf:file
PDF-format read length distribution as quality control
*_read_length_dist.pdf
metagene_profile_5p
*_metagene_profiles_5p.tsv:file
Metagene profile aligning with the start codon
*_metagene_profiles_5p.tsv
metagene_profile_3p
*_metagene_profiles_3p.tsv:file
Metagene profile aligning with the stop codon
*_metagene_profiles_3p.tsv
metagene_plots
*_metagene_plots.pdf:file
Metagene plots for quality control
*_metagene_plots.pdf
psite_offsets
*_psite_offsets.txt:file
“If the P-site offsets are not provided, txt file containing the derived relative offsets”
*_psite_offsets.txt
pos_wig
*_pos.wig:file
Positive strand WIG file for visualization in Genome Browser
*_pos.wig
neg_wig
*_neg.wig:file
Negative strand WIG file for visualization in Genome Browser
*_neg.wig
orfs
*_translating_ORFs.tsv:file
“TSV with ORFs assessed as translating in this BAM file. You can output all ORFs regardless of the translation status with option —report_all”
*_translating_ORFs.tsv
versions
versions.yml:file
File containing software versions
versions.yml
Python package to detect translating ORF from Ribo-seq data
