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NBISweden · Sep 17, 2024 · 00893a7 · 00893a7
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diff --git a/bin/agat_sp_compare_two_annotations.pl b/bin/agat_sp_compare_two_annotations.pl
@@ -729,18 +729,18 @@ =head1 DESCRIPTION
 
 =head1 SYNOPSIS
 
-    agat_sp_compare_two_annotations.pl -gff1 infile.gff [ -o outfile ]
+    agat_sp_compare_two_annotations.pl -gff1 infile1.gff -gff2 infile2.gff  [ -o outfile ]
     agat_sp_compare_two_annotations.pl --help
 
 =head1 OPTIONS
 
 =over 8
 
-=item B<-gff1>
+=item B<--gff1>
 
 Input GTF/GFF file1.
 
-=item B<-gff2>
+=item B<--gff2>
 
 Input GTF/GFF file2.
 

diff --git a/docs/tools/agat_sp_compare_two_annotations.md b/docs/tools/agat_sp_compare_two_annotations.md
@@ -3,15 +3,15 @@
 ## DESCRIPTION
 
 The script aims to compare two annotation of the same assembly. It provided
-information about split/fusion of genes between the two annotations.
-The most common case are:
-1 => 0 ( gene uniq to file1)
-0 => 1 ( gene uniq to file2)
-1 => 1 ( 1 gene from file 1 overlaps only 1 gene from file2)
-1 => &lt;many> ( 1 gene from file 1 overlaps &lt;many> genes from file2) => split case (with file 1 as reference)
+information about split/fusion of genes between the two annotations.  
+The most common case are:  
+1 => 0 ( gene uniq to file1)  
+0 => 1 ( gene uniq to file2)  
+1 => 1 ( 1 gene from file 1 overlaps only 1 gene from file2)  
+1 => &lt;many> ( 1 gene from file 1 overlaps &lt;many> genes from file2) => split case (with file 1 as reference)  
 &lt;many> => 1 ( &lt;many> genes from file 1 overlap only 1 gene from file2) => fusion case (with file 1 as reference)
 
-Then you can get more complex cases:
+Then you can get more complex cases:  
 &lt;many> => &lt;many>  (&lt;many> genes from file 1 overlap &lt;many> genes from file2)
 
 The script output a folder containing a report of number of different cases as well as a file
@@ -20,17 +20,17 @@ per case type listing per line the gene feature's ID involved in each case.
 ## SYNOPSIS
 
 ```
-agat_sp_compare_two_annotations.pl -gff1 infile.gff [ -o outfile ]
+agat_sp_compare_two_annotations.pl --gff1 infile1.gff -gff2 infile2.gff [ -o outfile ]
 agat_sp_compare_two_annotations.pl --help
 ```
 
 ## OPTIONS
 
-- **-gff1**
+- **--gff1**
 
     Input GTF/GFF file1.
 
-- **-gff2**
+- **--gff2**
 
     Input GTF/GFF file2.