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update doc #490

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Sep 17, 2024
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update doc #490

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6 changes: 3 additions & 3 deletions bin/agat_sp_compare_two_annotations.pl
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Expand Up @@ -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.

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20 changes: 10 additions & 10 deletions docs/tools/agat_sp_compare_two_annotations.md
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Expand Up @@ -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
Expand All @@ -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.

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