Description

Calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data

Input

name:type
description
pattern

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

bam{:bash}

:file

Transcriptome BAM file

*.{bam}

meta2{:bash}

:map

Map containing reference information for the reference genome GTF file e.g. [ id:'Ensembl human v.111' ]

gtf{:bash}

:file

GTF file of reference genome

*.{gtf.gz,gtf}

meta3{:bash}

:map

Map containing reference information for the reference genome FASTA file e.g. [ id:'Ensembl human v.111' ]

fasta{:bash}

:file

FASTA file of reference genome

*.{fasta,fa,fasta.gz,fa.gz}

Output

name:type
description
pattern

best_offset{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

*.best_offset.txt{:bash}

:file

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

offset{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

*.psite_offset.tsv{,.gz}{:bash}

:file

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

offset_plot{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

offset_plot/*{:bash}

:file

P-site offset plots for each read length (optional)

offset_plot/*

psites{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

*.psite.tsv{,.gz}{:bash}

:file

TSV file containing P-site transcriptomic coordinates and information for each alignment (optional)

*.psite.tsv.gz

codon_coverage_rpf{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

*.codon_coverage_rpf.tsv{,.gz}{:bash}

:file

TSV file with codon-level RPF coverage for each transcript (optional)

*.codon_coverage_rpf.tsv.gz

codon_coverage_psite{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

*.codon_coverage_psite.tsv{,.gz}{:bash}

:file

TSV file with codon-level P-site coverage for each transcript (optional)

*.codon_coverage_psite.tsv.gz

cds_coverage{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

*.cds_coverage_psite.tsv{,.gz}{:bash}

:file

TSV file with CDS P-site in-frame counts for each transcript (optional)

*.cds_coverage_psite.tsv.gz

cds_window_coverage{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

*nt_coverage_psite.tsv{,.gz}{:bash}

:file

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

ribowaltz_qc{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

ribowaltz_qc/*.pdf{:bash}

:file

riboWaltz diagnostic plots (optional)

ribowaltz_qc/*

ribowaltz_qc_data{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

ribowaltz_qc/*.tsv{:bash}

:file

TSV files containing data underlying riboWaltz QC plots including read length distribution, read length bins for P-site offset identification, ends heatmap, codon usage, P-site region distribution, frame distribution, frame distribution stratified by read length, and metaprofile P-site frequency around start/stop codons (optional)

ribowaltz_qc/*.tsv

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

Tools

ribowaltz
MIT

Calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data.

github.com/LabTranslationalArchitectomics/riboWaltz 10.1371/journal.pcbi.1006169
included in
riboseq
maintainer
Github user iraiosub
get in touch
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