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 Visualization and quality control.

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.