Update docs

tools/hicexplorer/hicBuildMatrixMicroC.xml

@@ -171,11 +171,10 @@ Creation of the contact matrix
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-**hicBuildMatrixMicroC** creates a contact matrix based on Micro-C read pairs. It requires two sam or bam files
-corresponding to the first and second mates of the paired-end Hi-C reads mapped on the reference genome.
-The sam and bam files should not be sorted by position. In difference to Hi-C, there is one option to create the Hi-C contact matrix, 
-by fixed bin size (eg. 10000 bp). Micro-C does not have restriction cut sites, therefore a resolution on with it is not possible.
-**hicBuildMatrixMicroC** generates a quality control output that can be used to analyze the quality of the Hi-C reads to assess if the experiment and sequencing were successful.
+**hicBuildMatrixMicroC** generates a contact matrix from Micro-C read pairs, using paired-end Hi-C reads mapped to a reference genome. This process requires two SAM or BAM files: one for the first mate and one for the second mate of the paired-end reads. These files must be unaligned by position (i.e., not sorted). Unlike traditional Hi-C data, where restriction enzyme cut sites determine resolution, Micro-C does not rely on such sites. Instead, the contact matrix is created using a fixed bin size (e.g., 10,000 bp). 
+
+Additionally, **hicBuildMatrixMicroC** produces a quality control report to evaluate the quality of the Hi-C reads, aiding in determining the success of both the experimental protocol and sequencing process.
+
 
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@@ -184,35 +183,37 @@ Usage
 -----
 
 
-This tool must be used on paired sam / bam files produced with a program that supports local alignment (e.g. Bowtie2) where both PE reads are mapped using the --local option.
+This tool is designed to work with paired SAM/BAM files generated by alignment software supporting local alignment, such as Bowtie2, using the `--local` alignment option for paired-end reads. Both files should represent properly mapped reads.
 
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 Output
 ------
 
-**hicBuildMatrixMicroC** creates multiple outputs:
+**hicBuildMatrixMicroC** generates the following outputs:
+
+- **Contact Matrix**: A matrix compatible with HiCExplorer for downstream analyses.
+- **Accepted Alignments BAM File**: This file includes valid Hi-C read pairs. While not directly used by HiCExplorer, it is valuable for inspecting the distribution of valid reads, such as around restriction enzyme sites, or for other analyses.
+- **Quality Control Report**: This report provides an evaluation of the Hi-C data, helping to determine whether the library preparation and experimental workflow were successful.
 
-    - The contact matrix used by HiCExplorer for all downstream analyses.
-    - A bam file with the accepted alignments, which can be useful to inspect the distribution of valid Hi-C reads pairs, notably around restriction enzyme sites or for other downstream analyses. This file is not used by any HiCExplorer tools.
-    - A quality control report to assess if the Hi-C protocol and library contrusction were successful.
 
 Example plot
 ++++++++++++
 
 .. image:: hicPlotMatrix.png
    :width: 50%
 
-Contact matrix of *Drosophila melanogaster* embryos built with **hicBuildMatrix**, for Micro-C data it looks similar, and visualized using ``hicPlotMatrix``. Hi-C matrix bins were merged to a 25 kb bin size before plotting using ``hicMergeMatrixBins``.
+*Contact matrix of *Drosophila melanogaster* embryos built using **hicBuildMatrix**. The example shows Micro-C data, visualized with `hicPlotMatrix`. Bins were merged to a 25 kb resolution using `hicMergeMatrixBins` before plotting.*
 
 
 
 
 Quality report
 ++++++++++++++
 
-A quality report is produced alongside the contact matrix, it is similar to the one from hicBuildMatrix. However, Micro-C has no restriction cut sites, therefore the restriction cut sites, dangling ends and self circles are not shown in the report.
+A detailed quality control report accompanies the contact matrix. This report is similar to the one generated by **hicBuildMatrix**, but excludes information specific to restriction cut sites, such as dangling ends and self-circles, as these features are not applicable to Micro-C data.
+
 
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