Juke34
commented
4 months ago Could you give a try, I made the modification in the agat_sp_compare_two_annotations_435 branch. In the environment containing all dependencies (eg from conda or container installation):
git clone https://github.com/NBISweden/AGAT.git
cd AGAT
git checkout agat_sp_compare_two_annotations_435
perl Makefile.PL
make
make test
make installthen you can execute as usual:
agat_sp_compare_two_annotations.pl --gff1 file1 --gff2 file2
Or:
git clone https://github.com/NBISweden/AGAT.git
cd AGAT
git checkout agat_sp_compare_two_annotations_435then execute using this syntax:
perl -I lib bin/agat_sp_compare_two_annotations.pl --gff1 file1 --gff2 file2
HouYan20
Dear Jacques, Thanks a lot for creating AGAT! It is a wonderful tool. Helped me a lot. Recently, I used "agat_sp_compare_two_annotations.pl" to compare my two genome annotation outputs, one with homology evidence, and another with RNA-seq evidence.
Could you please update the script to generate ID lists for each case of genes found by the script? I mean outputs like, uniq_gene_gff1.txt, uniq_gene_gff2.txt, overlap.txt, split.txt, fusion.txt
They could be just gene ID lists. Such as, when "> cat uniq_gene_file1.txt", got gene_A000001 gene_C000002
Or, could be gene position list. Such as, when ">cat uniq_gene_file1.txt", got Chr1 start end ChrX start end
I want these information because my two annotations have many differences (see following output), which is not a big surprise. However, I would like to know what they are.
For example, I would like to check whether the 6300 genes (as shown in the following table), which has no overlap with the RNA evidence, could have any function annotation in Nr blastp result. Also, I would like to extract the 5006 genes that only annotated by RNA evidence and make a blast analysis.
Looking forward to hearing from you! Thanks a lot in advance! Best, Yan