Visualization and QC¶
Use the interactive dashboards to facilitate quality control (QC) and Ribo-seq ORFs discovery, just follow the “hints”.
Important
To prepare the input for the dashboards, follow the instructions below. To use the quality control app, intermediate
files are required, i.e. the pipeline must have been run with the -k/--keep-intermediate-files flag.
How to prepare the input for the dashboards¶
Summarizing the profile construction¶
To prepare the input for the profile construction dashboard
summarize-rpbp-profile-construction [options] config
For all options, consult the API for summarize-rpbp-profile-construction.
Required input¶
Output files from the ORF profile construction step.
Expected output¶
The base path for these files is: <riboseq_data>/analysis/profile_construction.
<project_name>[.note].read-filtering-counts.csv.gz A CSV file with read counts after each step of the pipeline, one row per sample, with the following columns: “note” (sample name), “raw_data_count” (reads in the original FASTQ), “without_adapters_count” (reads remaining after running Flexbar), “without_rrna_count” (reads remaining after rRNA removal), “genome_count” (genome alignments), “unique_count” (unique genome alignments), “length_count” (periodic reads).
<project_name>[.note].length-distribution.csv.gz A CSV file with counts of aligned reads for each length, one row per sample.
<project_name>[.note][-unique].periodic-offsets.csv.gz A CSV file with all P-site offsets and read lengths for each samples.
<project_name>[.note][-unique].frame-counts.csv.gz A CSV file with P-site adjusted coverage across 3 frames summed across all ORFs for each sample.
Summarizing the Rp-Bp predictions¶
To prepare the input for the predictions dashboard
summarize-rpbp-predictions [options] config
For all options, consult the API for summarize-rpbp-predictions.
Required input¶
Output files from the Translation prediction step.
Expected output¶
The base path for these files is: <riboseq_data>/analysis/rpbp_predictions.
<project_name>[.note][-unique][.filtered].predicted-orfs.bed.gz A BED12+ file with the combined predicted translation events (Ribo-seq ORFs) from all samples and replicates. Additional columns include sample or replicate, Bayes factor mean and variance, P-site coverage across 3 frames, ORF number, ORF length, label, host transcript biotype, and associated gene id, name and biotype, and compatible transcripts.
<project_name>[.note][-unique][.filtered].igv-orfs.bed.gz A BED12 file with all unique Ribo-seq ORFs.
<project_name>.summarize_options.json A json summary file for the app.
<genome_name>.circos_graph_data.json A json file with the ORF distribution across chromosomes for the app.
Hint
The file <project_name>[.note][-unique][.filtered].predicted-orfs.bed.gz has a final output combining all predictions across your samples and/or replicates (including Bayes factor mean and variance for each sample, etc.). If you need a unique list of Ribo-seq ORFs (only coordinates i.e standard BED12, without duplicated entries for samples and/or replicates), use <project_name>[.note][-unique][.filtered].igv-orfs.bed.gz.
How to launch the web applications¶
Attention
For the apps, the configuration file is passed via a (required) named argument using -c/–config.
Tip
Any of the above command will open a browser page with the web application running locally. You can also specify a --host and a --port, e.g. if launching the app from a remote server use --host 0.0.0.0, then open a page on http://X.X.X.X:8050 where X.X.X.X is the public IP of your remote server.
Ribo-seq quality control¶
To launch the profile construction dashboard
rpbp-profile-construction-dashboard [options] -c CONFIG
The application has multiple views to facilitate quality control, e.g.
For all options, consult the API for rpbp-profile-construction-dashboard.
Ribo-seq ORFs discovery¶
To launch the predictions dashboard
rpbp-predictions-dashboard [options] -c CONFIG
The application has multiple views to facilitate ORF discovery, including an integrated IGV browser for the visual exploration of predicted Ribo-seq ORFs, e.g.
Try it out, and see more! For all options, consult the API for rpbp-predictions-dashboard.