Frequently asked questions

I don’t want/I can’t install it on my computer. Can I still use Rp-Bp without installing the package?

Yes, you can use a Docker or a Singularity container. Simply pull, and you’re done! See Installation for instructions. Example calls are also given in the user guide and tutorials.

How do I launch the app remotely?

By default, the application is opened in a browser page on localhost:8050. You don’t have to actually worry about this. But you can also specify a --host and a --port when calling the app, enabling you to launch it from a remote server. In the latter case, however, you have to open a browser page at the correct address. For example, if you use --host 123.123.123.123, then open a page on http://123.123.123.123:8050/. To launch the app from a container, see How to use the containers.

Why is the ORF label not consistent with the host transcript?

In some cases, the ORF label may not be consistent with the host transcript, as reported by the ORF “id” (transcript_seqname:start-end:strand). To resolve such seemingly incoherent assignments, compatible transcripts are reported for each ORF in <genome_name>.orfs-labels.annotated[.orf_note].tab.gz and shown in the prediction dashboard, see More about annotations.

I have my own alignments, can I use Rp-Bp?

The short answer is yes. The pipeline is designed to handle all steps from raw FASTQ files up to the final list of translated Ribo-seq ORFs, but you can start the pipeline from any step. Check the tutorial How to use existing alignment files.

I get errors when calling summarize-rpbp-predictions

The most common errors e.g. AttributeError: 'float' object has no attribute 'left' are due to the bin width for the Circos plot. Try reducing it using --circos-bin-width VALUE (default VALUE: 10000000). You may also have to use --circos-show-chroms if your organism has a different nomenclature. Use summarize-rpbp-predictions --help for details.

The IGV browser does not load or the predictions app fails to start

The most likely reason is that your reference genome sequence (given by the config key fasta) is not indexed, i.e the file *.fasta.fai is missing. You can create the missing index using samtools faidx.

I get RuntimeWarning: invalid value encountered in divide res, _ = _lowess(y, x, x, np.ones_like(x),

This happens for 3 nt ORFs.

Can Rp-Bp handle matched RNA-seq data?

No, but if you have matched RNA-seq data, you can generate a de novo assembly, which can be used by Rp-Bp, see More about de novo ORF discovery. Check Ribotools for translation efficiency (TE) and differential expression (DE) analyses using matched Ribo-seq and/or RNA-seq data. It uses Rp-Bp for periodicity estimation, and follows the same alignment workflow, directory structure, and naming convention. It can also use the output of Rp-Bp directly, handling separately the RNA-seq data, and combines the results for TE analysis.