@@ -6,29 +6,29 @@ This project is young and in development, some errors will be corrected, improve
## Usage
GrAnnoT requires the graph to be in GFA format with W-lines that describe the walks of the input genomes. For example minigraph-cactus gives that kind of output.
You first need to extract from the GFA the positions of the segments of the graph on the genomes it contains. For this you need to run the script getSegmentsCoordinates.py with the GFA file as input.
Then you will need to run the following command using the segments coordinates on the reference genome (for the annotation), and the annotation file in GFF/GTF format :
```
bedtools intersect -wo -a segmentsCoordinatesOnReferenceGenome.bed -b annotationFile.gff > intersectFile.bed
```
You can then finally run GrAnnoT itself via the script main.py with the following arguments :
- intersect file
You can run GrAnnoT via the script main.py with the following arguments :
- GFA file with walks
- bed file with coordinates of the segments on the target genome
- the name of the target genome path in the GFA file.
- annotation file of a genome embedded in the graph
- the name of the source genome, that the annotation file refers to
- optionnaly the names of the target genomes (these names must be included in the walks of the graph). If no name is specified, the annotation will be transfered on all the genomes in the graph.
The other options can be found if you run "main.py -h".
It will output the following files :
For the graph :
- a GFF and a GAF file with the annotation of the graph
- the GFF file with the annotation of the target genome
- a text file with the details of the variations within the annotated regions.
For each target genome :
- the GFF file with the annotation of the target genome
- a text file with the details of the variations within the annotated regions
- a text file with the alignments of the genes from the source genome and from the target genome
### Support
## Support
If you have any question or suggestion, feel free to contact me by email : nina.marthe@ird.fr
### Authors
## Authors
If you use this program please cite Nina Marthe, Francois Sabot and Matthias Zytnicki.
