[MODIF] update docs

docs/output.md

@@ -109,8 +109,8 @@ can thus be discarded using the `--min_cis_dist` parameter.
 - `*.FiltPairs` - List of filtered pairs
 - `*RSstat` - Statitics of number of read pairs falling in each category
 
-Of note, these results are saved only if `--save_pairs_intermediates` is used.
-The validPairs are stored using a simple tab-delimited text format ;
+Of note, these results are saved only if `--save_pairs_intermediates` is used.  
+The `validPairs` are stored using a simple tab-delimited text format ;
 
 ```bash
 read name / chr_reads1 / pos_reads1 / strand_reads1 / chr_reads2 / pos_reads2 /
@@ -131,9 +131,9 @@ recommanded as this pairs are likely to be self ligation products.
 
 #### Duplicates removal
 
-Note that validPairs file are generated per reads chunck (and saved only if
+Note that `validPairs` file are generated per reads chunck (and saved only if
 `--save_pairs_intermediates` is specified).
-These files are then merged in the allValidPairs file, and duplicates are
+These files are then merged in the `allValidPairs` file, and duplicates are
 removed (see `--keep_dups` to disable duplicates filtering).
 
 **Output directory: `results/hicpro/valid_pairs`**
@@ -146,7 +146,7 @@ We usually expect to see a distribution centered around 300 pb which correspond
 to the paired-end insert size commonly used.
 The fraction of dplicates is also presented. A high level of duplication
 indicates a poor molecular complexity and a potential PCR bias.
-Finaly, an important metric is to look at the fraction of intra and
+Finally, an important metric is to look at the fraction of intra and
 inter-chromosomal interactions, as well as long range (>20kb) versus short
 range (<20kb) intra-chromosomal interactions.
 
@@ -221,16 +221,16 @@ downstream analysis.
 ## 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.  
+The .cool and .hic format are compressed and indexed and usually much more efficient that the txt format.  
 In the current workflow, we propose to use the `cooler` format as a standard to build the raw and normalized maps
 after valid pairs detection as it is used by several downstream analysis and visualization tools.
 
 Raw contact maps are therefore in **`results/contact_maps/raw`** which contains the different maps in `txt` and `cool` formats, at various resolutions.
 Normalized contact maps are stored in **`results/contact_maps/norm`** which contains the different maps in `txt`, `cool`, and `mcool` format.
-The bin coordinates used for the various resolution are available in **`results/contact_maps/bins`**.
+The bin coordinates used for all resolutions are available in **`results/contact_maps/bins`**.
 
 Note that `txt` contact maps generated with `cooler` are identical to those generated by `HiC-Pro`.
-However, differences can be observed on the normalized contact maps as the balancing algorithm is not the same.
+However, differences can be observed on the normalized contact maps as the balancing algorithm is not exactly the same.
 
 ## Downstream analysis