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NBISweden · Apr 15, 2021 · 9668b12 · 9668b12
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diff --git a/docs/index.rst b/docs/index.rst
@@ -23,7 +23,7 @@ Contents
    troubleshooting.md
 
 .. toctree::
-   :maxdepth: 0
+   :maxdepth: 1
    :caption: List of tools:
 
    tools/agat_convert_bed2gff.md

diff --git a/docs/topological-sorting-of-gff-features.md b/docs/topological-sorting-of-gff-features.md
@@ -27,7 +27,7 @@ Zhigang Lu has made a nice post about his experience trying to find a way to get
      * [gffread](#gffread-2)
 
 
-#### Tests summary
+## Tests summary
 
 tool | option in command line | Type of sorting | Comment
 -- | -- | -- | -- |
@@ -37,7 +37,7 @@ tool | option in command line | Type of sorting | Comment
 [GFF3sort](https://github.com/billzt/gff3sort) | --precise | by chromosomes and positions then attribute with Parent attribute first.  | move lines with "Parent=" attributes (case insensitive) behind lines without "Parent=" attributes. The goal of GFF3sort is not to obtain a topological sorting but rather getting something that could be indexed optimally by third part tools.
 [gffread](https://github.com/gpertea/gffread) | | By default, chromosomes are kept in the order they were found. With --sort-alpha parameter the chromosomes (reference sequences) are sorted alphabetically | /!\ Some feature types are lost e.g. `gene`, `three_prime_UTR`, `five_prime_UTR`, etc...
 
-### Example 1
+## Example 1
 
 This test is based on the file used by [Zhigang Lu](https://zhiganglu.com/post/sort-gff-topologically/)
 
@@ -269,7 +269,7 @@ SM_V7_1	AUGUSTUS	CDS	145395	145678	.	-	2	Parent=Smp_315690.2
 SM_V7_1	AUGUSTUS	CDS	151075	151132	.	-	0	Parent=Smp_315690.2
 ```
 
-### Example 2
+## Example 2
 
 This test is based on the file used by [GFF3sort](https://github.com/billzt/gff3sort)
 

diff --git a/docs/troubleshooting.md b/docs/troubleshooting.md
@@ -1,6 +1,6 @@
 # Troubleshooting
 
-# AGAT throws features out, because the feature type is not yet taken into account
+## AGAT throws features out, because the feature type is not yet taken into account
 Feature types (primary_tag) handled by AGAT are defined within json files. Most common features are already defined in those files. If you encounter files with feature types not accepted, AGAT will inform you and throw the features out. To keep those feature you must inform properly AGAT how to handle them.
 First access the json files by running:
 ```
@@ -31,7 +31,7 @@ Where `bigRNA`is the feature type and `gene`the parent feature type expected.
  * standalone: feature does not expect children
  * other values do not have any meaning but a value is required, write whatever you want.
 
-# AGAT throws features out, because child features are not provided
+## AGAT throws features out, because child features are not provided
 Features level1 (e.g. gene, match, chromosome) may require to have child features or not depending of the information stored into the `features_level1.json` file. If a child is required, and the GFF file does not contain it, the level1 feature will be thrown away. You must modify the json file to add the the term `standalone` to inform AGAT that this feature level1 do not require any child. (This work only on feature level1, not level2 or level3). To access the json files run the following command:
 ```
 # export the json files