Description

Accurate detection of short and long active ORFs using Ribo-seq data

Input

Name (Type)
Description
Pattern

meta (map)

Map containing riboseq sample information
e.g. `[ id:‘sample1’, single_end

, strandedness: ‘single’ ]

bam_ribo (file)

Sorted riboseq BAM file(s)

*.{bam}

bai_ribo (file)

Index for sorted riboseq bam file(s)

*.{bai}

meta2 (map)

Map containing reference information for the candidate ORFs
e.g. [ id:'Ensembl human v.111' ]

candidate_orfs (file)

TSV file with candidate ORFs from ‘ribotricer prepareorfs’

*.tsv

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing riboseq sample information
e.g. `[ id:‘sample1’, single_end

]

protocol (file)

txt file containing inferred protocol if it was inferred (not supplied as input)

*_protocol.txt

bam_summary (file)

Text summary of reads found in the BAM

*_bam_summary.txt

read_length_dist (file)

PDF-format read length distribution as quality control

*_read_length_dist.pdf

metagene_profile_5p (file)

Metagene profile aligning with the start codon

*_metagene_profiles_5p.tsv

metagene_profile_3p (file)

Metagene profile aligning with the stop codon

*_metagene_profiles_3p.tsv

metagene_plots (file)

Metagene plots for quality control

*_metagene_plots.pdf

psite_offsets (file)

“If the P-site offsets are not provided, txt file containing the
derived relative offsets”

*_psite_offsets.txt

pos_wig (file)

Positive strand WIG file for visualization in Genome Browser

*_pos.wig

neg_wig (file)

Negative strand WIG file for visualization in Genome Browser

*_neg.wig

orfs (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 (file)

File containing software versions

versions.yml
included in
riboseq
maintainer
Github user pinin4fjords
get in touch
Ask a question on Slack Open an issue on GitHub

Tools

ribotricer
GNU General Public v3 (GPL v3)

Python package to detect translating ORF from Ribo-seq data

github.com/smithlabcode/ribotricer 10.1093/bioinformatics/btz878