Description

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

Input

name:type
description
pattern

meta:map

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

bam:file

Transcriptome BAM file

*.{bam}

meta2:map

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

gtf:file

GTF file of reference genome

*.{gtf.gz,gtf}

meta3:map

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

fasta:file

FASTA file of reference genome

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

Output

name:type
description
pattern

best_offset

meta:map

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

*.best_offset.txt: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

meta:map

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

*.psite_offset.tsv{,.gz}: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

meta:map

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

offset_plot/*:file

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

offset_plot/*

psites

meta:map

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

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

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

*.psite.tsv.gz

codon_coverage_rpf

meta:map

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

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

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

*.codon_coverage_rpf.tsv.gz

codon_coverage_psite

meta:map

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

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

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

*.codon_coverage_psite.tsv.gz

cds_coverage

meta:map

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

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

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

*.cds_coverage_psite.tsv.gz

cds_window_coverage

meta:map

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

*nt_coverage_psite.tsv{,.gz}: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

meta:map

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

ribowaltz_qc/*.pdf:file

riboWaltz diagnostic plots (optional)

ribowaltz_qc/*

versions

versions.yml: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
Github user iraiosub
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