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