INSTRUCTIONS FOR THE TOOL vis-rRNA-QC

Components: Pipeline: quality_control_and_depletion_analysis.nf Visualization: app.py

Prerequisites

1. Get the repository on your local machine
2. Install the environment manager conda https://docs.conda.io/projects/conda/en/stable/
3. Install Python
4. Install the folowing Python Packages with pip:
   • dash
   • dash-bootstrap-components
   • dash-core-components
   • dash-html-components
   • dash-table
   • pandas
   • plotly
   • numpy
5. rRNA-genes file 'rRNA_genes_type.txt' Format: gene_id,type SCOr01,5S SCOr02,23S SCOr03,16S

Pipeline Instructions

• Command for execution The command can only be executed if you are in the same folder as the pipeline quality_control_and_depletion_analysis.nf
  nextflow run quality_control_and_depletion_analysis.nf --reads "fastq.gz" --reference <.fna.gz> --gff <*.gff.gz> --rRNAgenes rRNA_genes_type.txt -profile conda Note: The read files and the rRNA_genes_type.txt file need to be in the same directory as the pipeline
• Additional parameters --paired Paired end reads --noQuali Disable quality control --noQualiRNA Disable quality control RNASeq --noCounts Disable feature counts --noDepletionQC Disable depletion Analysis --featureCountsS FeatureCounts attribute strandedness: unstranded, reverse or forward strandness (default: reverse) --g FeatureCounts attribute to group features (default: locus_tag) --t FeatureCounts attribute that should be counted (default: transcript) --extraAttributes FeatureCounts extra attriutes divided by comma (default: gene_name) --M FeatureCounts: Count multi-mapping reads --O FeatureCounts: Count reads overlapping features --fraction FeatureCounts: Fractional counts for multi-mapping/overlapping features (must be used together with -M or -O)

Visualization Instructions

• Command for execution: The command can only be executed if you are in the same folder as the app.py file, in this case you have to move to the 'bin' folder python3 app.py

  Output example: Dash is running on http://127.0.0.1:8050/

• Serving Flask app 'app'
• Debug mode: on

• After running th command above, the Dash app is running under the address displayed in the command line example: http://127.0.0.1:8050/ Link can be opend with any browser