diff --git a/README.md b/README.md
index 9ba1078d093723191c746198725674ee1384ab8e..73e2665b84470263b8d20c128cba22be7db2d6ae 100644
--- a/README.md
+++ b/README.md
@@ -46,8 +46,8 @@ results highly reproducible.
 4. Export to various contact maps formats ([`HiC-Pro`](https://github.com/nservant/HiC-Pro), [`cooler`](https://github.com/open2c/cooler))
 5. Quality controls ([`HiC-Pro`](https://github.com/nservant/HiC-Pro), [`HiCExplorer`](https://github.com/deeptools/HiCExplorer))
 6. Compartments calling ([`cooltools`](https://cooltools.readthedocs.io/en/latest/))
-8. TADs calling ([`HiCExplorer`](https://github.com/deeptools/HiCExplorer), [`cooltools`](https://cooltools.readthedocs.io/en/latest/))
-9. Quality control report ([`MultiQC`](https://multiqc.info/))
+7. TADs calling ([`HiCExplorer`](https://github.com/deeptools/HiCExplorer), [`cooltools`](https://cooltools.readthedocs.io/en/latest/))
+8. Quality control report ([`MultiQC`](https://multiqc.info/))
 
 ## Quick Start
 
diff --git a/docs/output.md b/docs/output.md
index 342ce3a704e7d0cdf6ba5fed8f28c00a0d4d8f1f..d73bce332fae54e6248816828b963d38b24f5eac 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -15,7 +15,7 @@ and processes data using the following steps:
   * [Valid pairs detection](#valid-pairs-detection)
   * [Duplicates removal](#duplicates-removal)
   * [Contact maps](#hicpro-contact-maps)
-* [Contact maps](#contact-maps)
+* [Hi-C contact maps](#hic-contact-maps)
 * [Downstream analysis](#downstream-analysis)
   * [Distance decay](#distance-decay)
   * [Compartments calling](#compartments calling)
@@ -193,7 +193,7 @@ files.
 This format is memory efficient, and is compatible with several software for
 downstream analysis.
 
-## Contact maps
+## Hi-C contact maps
 
 Contact maps are usually stored as simple txt (`HiC-Pro`), .hic (`Juicer/Juicebox`) and .(m)cool (`cooler/Higlass`) formats.
 Note that .cool and .hic format are compressed and usually much more efficient that the txt format.  
@@ -227,6 +227,7 @@ Although different methods have been proposed for compartment calling, the stand
 Here, we use the implementation available in the [`cooltools`](https://cooltools.readthedocs.io/en/lates) package.
 
 Results are available in **`results/compartments/`** folder and includes :
+
 * `*cis.vecs.tsv`: eigenvectors decomposition along the genome
 * `*cis.lam.txt`: eigenvalues associated with the eigenvectors
 
@@ -236,9 +237,11 @@ TADs has been described as functional units of the genome.
 While contacts between genes and regulatority elements can occur within a single TADs, contacts between TADs are much less frequent, mainly due to the presence of insulation protein (such as CTCF) at their boundaries. Looking at Hi-C maps, TADs look like triangles around the diagonal. According to the contact map resolutions, TADs appear as hierarchical structures with a median size around 1Mb (in mammals), as well as smaller structures usually called sub-TADs of smaller size.
 
 TADs calling remains a challenging task, and even if many methods have been proposed in the last decade, little overlap have been found between their results.
+
 Currently, the pipeline proposes two approaches :
-- Insulation score using the [`cooltools`](https://cooltools.readthedocs.io/en/latest/cli.html#cooltools-diamond-insulation) package. Results are availabe in **`results/tads/insulation`**.
-- [`HiCExplorer TADs calling`](https://hicexplorer.readthedocs.io/en/latest/content/tools/hicFindTADs.html). Results are available at **`results/tads/hicexplorer`**.
+
+* Insulation score using the [`cooltools`](https://cooltools.readthedocs.io/en/latest/cli.html#cooltools-diamond-insulation) package. Results are availabe in **`results/tads/insulation`**.
+* [`HiCExplorer TADs calling`](https://hicexplorer.readthedocs.io/en/latest/content/tools/hicFindTADs.html). Results are available at **`results/tads/hicexplorer`**.
 
 Usually, TADs results are presented as simple BED files, or bigWig files, with the position of boundaries along the genome.
 
diff --git a/docs/usage.md b/docs/usage.md
index 3c39e290986aa5f0efc59c628bac3c2984c8c186..f072ba565b84454879b8f1e9f83cf368f74ae24f 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -398,7 +398,6 @@ Default: 'AAGCTAGCTT'
 
 Exemple of the ARIMA kit: GATCGATC,GANTGATC,GANTANTC,GATCANTC
 
-
 ### DNAse Hi-C
 
 #### `--dnase`