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:false, strandedness: ‘single’ ]
bam
:file
BAM/CRAM/SAM file
*.{bam,cram,sam}
bai
Index for sorted BAM/CRAM/SAM file
*.{bai}
strandedness
:string
Strandedness of the data
meta2
Map containing reference information for the candidate ORFs e.g. [ id:'Ensembl human v.111' ]
[ id:'Ensembl human v.111' ]
candidate_orfs
TSV file with candidate ORFs from ‘ribotricer prepareorfs’
*.tsv
protocol
Groovy Map containing riboseq sample information e.g. `[ id:‘sample1’, single_end:false ]
*_protocol.txt
txt file containing inferred protocol if it was inferred (not supplied as input)
bam_summary
*_bam_summary.txt
Text summary of reads found in the BAM
read_length_dist
*_read_length_dist.pdf
PDF-format read length distribution as quality control
metagene_profile_5p
*_metagene_profiles_5p.tsv
Metagene profile aligning with the start codon
metagene_profile_3p
*_metagene_profiles_3p.tsv
Metagene profile aligning with the stop codon
metagene_plots
*_metagene_plots.pdf
Metagene plots for quality control
psite_offsets
*_psite_offsets.txt
“If the P-site offsets are not provided, txt file containing the derived relative offsets”
pos_wig
*_pos.wig
Positive strand WIG file for visualization in Genome Browser
neg_wig
*_neg.wig
Negative strand WIG file for visualization in Genome Browser
orfs
*_translating_ORFs.tsv
“TSV with ORFs assessed as translating in this BAM file. You can output all ORFs regardless of the translation status with option –report_all”
versions_ribotricer
${task.process}
The name of the process
ribotricer
The name of the tool
ribotricer --version 2>&1 | sed -n 's/^ribotricer, version //p'
:eval
The expression to obtain the version of the tool
versions
Python package to detect translating ORF from Ribo-seq data
