HRIBO
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Documentation
HRIBO
Additional information
Workflow configuration
Analysis result files
Metagene profiling
Example
Example workflow
Extended workflow
FAQ
Frequently asked questions
HRIBO
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HRIBO
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Documentation
HRIBO
Introduction
Requirements
Tools
miniconda3
HRIBO
snakemake
Input files
annotation.gff and genome.fa
input .fastq files
Sample sheet and configuration file
cluster.yaml
Output files
Single-file Output
Multi-file Output
Tool Parameters
Report
Example-workflow
References
Additional information
Workflow configuration
Default workflow
Biology Settings
adapter sequence
genome file
annotation file
sample sheet
alternative start codons
Differential Expression Settings
differentialexpression
features
contrasts
adjusted pvalue cutoff
log2 fold change cutoff
ORF predictions
Read statistics Settings
Metagene Profiling Settings
Positions outside of the ORF
Positions inside of the ORF
Filtering Methods
Neighboring Genes Distance
RPKM Threshold
Length Cutoff
Mapping Methods
Read Lengths:
Normalization Methods
Output Formats
PlotlyJS
Colors
Paired-end support
Analysis result files
ORF Predictions
predictions_reparation.xlsx
predictions_reparation.gff
predictions_deepribo.xlsx
predictions_deepribo.gff
Quality control
multiqc_report.html
heatmap_SpearmanCorr_readCounts.pdf
annotation_total.xlsx
total_read_counts.xlsx
annotation_unique.xlsx
unique_read_counts.xlsx
genome-browser
updated_annotation.gff
potentialStartCodons.gff
potentialStopCodons.gff
potentialRibosomeBindingSite.gff
potentialAlternativeStartCodons.gff
BigWig coverage files
Differential Expression
deltate/<contrast>_sorted.xlsx
riborex/<contrast>_sorted.xlsx
xtail/<contrast>_sorted.xlsx
xtail/r_<contrast>.pdf
xtail/fc_<contrast>.pdf
output tables
Metagene Profiling Analysis
Additional output
samples.xlsx
manual.pdf
overview.xlsx
Metagene profiling
What is metagene profiling?
Metagene output
Example output
Example
Example workflow
Setup
Retrieve and prepare input files
Annotation and genome files
.fastq files
Sample sheet and configuration file
Running the workflow
Run the workflow locally
Run Snakemake in a cluster environment
Example: Run Snakemake in a cluster environment
Results
Runtime
References
Extended workflow
Setup
Retrieve and prepare input files
Annotation and genome files
.fastq files
Sample sheet and configuration file
Running the workflow
Run the workflow locally
Run Snakemake in a cluster environment
Example: Run Snakemake in a cluster environment
Results
Runtime
References
FAQ
Frequently asked questions
Q: When using singularity I get
ERROR
:
Failed
to
set
effective
UID
to
0
.
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