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Fix Core and How_to
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strambc committed Sep 13, 2024
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4 changes: 2 additions & 2 deletions docs/source/core.rst
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Expand Up @@ -17,7 +17,7 @@ In this table, each row reports the ``X``, ``Y``, ``Z`` localization, and the Tr
In this table the reported ``X``, ``Y``, ``Z`` coordinates are assumed to result from post-processing and quality control procedures and therefore
correspond to the final localization of the DNA target under study.

.. tip:: The 4DN Data Portal only accepts GRCh38 for human and GRCm38 for mouse. For other species follow these `instructions. <https://data.4dnucleome.org/search/?type=Organism>`_ In case the genome under study contains an INSERTION/DELETION follow the instructions below.
.. tip:: The 4DN Data Portal only accepts GRCh38 for human and GRCm38 for mouse. For other species follow these `instructions. <https://data.4dnucleome.org/search/?type=Organism>`_ In addition, in case the genome under study contains INSERTION/DELETIONs follow also these :ref:`IN_DEL-reference-label`.

At a minimum the Table has to have 8 columns in the following order:
``Spot_ID``, ``Trace_ID``, ``X``, ``Y``, ``Z``, ``Chrom``, ``Chrom_Start``,
Expand Down Expand Up @@ -88,7 +88,7 @@ Example without INSERTION/DELETION
Example with INSERTION/DELETION
-------------------------------

.. warning:: In case your reference genome has insertions or deletions, please remember to follow all instructions listed here :ref:`IN_DEL-reference-label`
.. warning:: In case your reference genome has insertions or deletions, please remember to follow these :ref:`IN_DEL-reference-label`

.. include:: examples/core_IN-DEL
:code:
2 changes: 2 additions & 0 deletions docs/source/how_to_use.rst
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Expand Up @@ -4,6 +4,8 @@ To facilitate adoption of the FOF-CT format, table Templates can be dowloaded fr

These templates can be used as a starting point for filling in all the required :ref:`headers-reference-label` lines and :ref:`columns-reference-label`.

.. tip:: The 4DN Data Portal only accepts GRCh38 for human and GRCm38 for mouse. For other species follow these `instructions. <https://data.4dnucleome.org/search/?type=Organism>`_ In addition, in case the genome under study contains INSERTION/DELETIONs follow also these :ref:`IN_DEL-reference-label`.

The following is a short step-by-step description of how to use these templates:

#. Download the Templates package
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