From 00893a7ab867d3f92a8439fdd40cca276f8105dd Mon Sep 17 00:00:00 2001 From: Jacques Dainat Date: Tue, 17 Sep 2024 10:04:32 +0200 Subject: [PATCH] update doc --- bin/agat_sp_compare_two_annotations.pl | 6 +++--- docs/tools/agat_sp_compare_two_annotations.md | 20 +++++++++---------- 2 files changed, 13 insertions(+), 13 deletions(-) diff --git a/bin/agat_sp_compare_two_annotations.pl b/bin/agat_sp_compare_two_annotations.pl index 7c7a5ff8..e2a94723 100755 --- 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 index c990af48..82234bc6 100644 --- 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 => <many> ( 1 gene from file 1 overlaps <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 => <many> ( 1 gene from file 1 overlaps <many> genes from file2) => split case (with file 1 as reference) <many> => 1 ( <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: <many> => <many> (<many> genes from file 1 overlap <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.