Frequently asked questions
==========================

* :ref:`q1`
* :ref:`q2`
* :ref:`q3`
* :ref:`q4`
* :ref:`q5`
* :ref:`q6`
* :ref:`q7`
* :ref:`q8`

.. _q1:

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 :ref:`installation_full` for instructions.
Example calls are also given in the user guide and tutorials.

.. _q2:

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 :ref:`tutorial_containers`.

.. _q3:

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 :ref:`rpbp_genome`.

.. _q4:

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 :ref:`existing_alignment`.


.. _q5:

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 <http://circos.ca/>`_ 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.

.. _q6:

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 <http://www.htslib.org/doc/samtools-faidx.html>`_.


.. _q7:

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

This happens for 3 nt ORFs.

.. _q8:

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 :ref:`denovo`. Check
`Ribotools <https://ribotools.readthedocs.io/en/latest/index.html>`_ 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.