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dieterich-lab · Jan 13, 2024 · 1b9c476 · 1b9c476
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diff --git a/docs/.buildinfo b/docs/.buildinfo
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+# Sphinx build info version 1
+# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: fca39493043894451b87c0aa22d4a7c1
+tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/_sources/bedrmod.rst.txt b/docs/_sources/bedrmod.rst.txt
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+
+Data Specification
+===================
+
+Current version v1.7, consult `bedRMod <https://github.com/anmabu/bedRMod/tree/main>`_. The file extension is ".bed" or ".bedrmod".
+
+Notes
+------
+
+Additional columns
+^^^^^^^^^^^^^^^^^^^
+
+Users can add any number of additional columns to suit their needs (same as for BED), but these are ignored in Sci-ModoM. Note however that a bedRMod file with exactly 12 columns may be implicitely assumed to be a BED12 file by some software (bedtools, genome browsers, ...).
+
+Unmodified bases
+^^^^^^^^^^^^^^^^^
+
+bedRMod is a format to store modification data (site-specific or not), hence unmodified bases should not be recorded.
+Context can be recorded using chromStart/End + thickStart/End, additional columns, *etc*.
+
+General remarks
+^^^^^^^^^^^^^^^^
+
+In Sci-ModoM, uploading data in bedRMod format requires each bedRMod to contain a single organism (species and cell, tissue, or organ) and a single technology. One bedRMod file can however contain more than one modification, as recorded by column 4.
+
+If you file bedRmod file contains different data and/or additional columns to store information such as RNA type, experimental condition, *etc.*, you need to split your data such that individual bedRMod files can be uploaded with as much specific information as possible, *e.g. m6A in human cell type X using technology Y under treatment condition Z, etc.*
diff --git a/docs/_sources/database.rst.txt b/docs/_sources/database.rst.txt
diff --git a/docs/_sources/index.rst.txt b/docs/_sources/index.rst.txt
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+.. SciModoM-server documentation master file, created by
+   sphinx-quickstart on Wed Sep 20 13:37:03 2023.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to SciModoM-server's documentation!
+===========================================
+
+.. toctree::
+   :titlesonly:
+
+   database
+   bedrmod
+
+
+.. Indices and tables
+.. ==================
+..
+.. * :ref:`genindex`
+.. * :ref:`modindex`
+.. * :ref:`search`