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6 changes: 3 additions & 3 deletions doc/tutorial/cli.rst
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Expand Up @@ -7,7 +7,7 @@ Introduction
------------

After you have velocyto correctly installed on your machine (see :ref:`installation tutorial <install>`) the ``velocyto`` command will become available in the terminal.
``velocyto`` is a command line tool with subcomands. You can get info on all the available commands typing ``velocyto --help``. You will get the following output:
``velocyto`` is a command line tool with subcommands. You can get info on all the available commands typing ``velocyto --help``. You will get the following output:

.. include:: ../substitutions/velocyto.txt

Expand Down Expand Up @@ -54,14 +54,14 @@ The general signature for the ``run`` subcommand is:
Execution time is ~3h for a typical sample but might vary significantly by sequencing depth and cpu power.

.. warning::
Running velocyto without specifying a filtered barcode set (:code:`-b/--bcfile` option) is not recommended, do it at your own risk. In thsi way, the counter will use all the cell barcodes it encounters. It might result in long runtimes, large memory alloactions and big output matrix.
Running velocyto without specifying a filtered barcode set (:code:`-b/--bcfile` option) is not recommended, do it at your own risk. In this way, the counter will use all the cell barcodes it encounters. It might result in long runtimes, large memory allocations and big output matrix.


Notes on ``velocyto run``
~~~~~~~~~~~~~~~~~~~~~~~~~

As one of its first steps ``velocyto run`` will try to create a copy of the input .bam files sorted by cell-barcode. The sorted .bam file will be placed in the same directory as the original file and it will be named ``cellsorted_[ORIGINALBAMNAME]``.
The sorting procedure uses ``samtools sort`` and it is expected to be time consumning, because of this, the procedurre is perfomed in parellel by default. It is possible to control this parallelization using the parameters ``--samtools-threads`` and ``--samtools-memory``.
The sorting procedure uses ``samtools sort`` and it is expected to be time consuming, because of this, the procedure is perfomed in parallel by default. It is possible to control this parallelization using the parameters ``--samtools-threads`` and ``--samtools-memory``.

.. note::
If the file ``cellsorted_[ORIGINALBAMNAME]`` exists, the sorting procedure will be skipped and the file present will be used.
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