Sara Oppenheim

Thanks for your response! I've just added sortme to my QC pipeline, but below is what I currently do. The problem is that with the process starts from zero after...

Additional errors: Problem ! protein ID not found into the protein fasta file! Use of uninitialized value $prot_tag in concatenation (.) or string at /home/soppenheim/mendel-nas1/miniconda3/envs/agat/bin/agat_sp_load_function_from_protein_align.pl line 1000. We cannot check...

Hi Jaques, I'm going to try an exonerate run and I've installed the missing dependency. In the meantime, here are some lines from my pblat-based gff: ``` Aatri_ctg9 BLAT match_part...

Follow up: when I tried installing perl-xml-twig in my agat env, I got "All requested packages already installed." On Fri, Aug 6, 2021 at 1:01 PM Sara Oppenheim ***@***.***> wrote:...

I now have some exonerate output but I'm still getting errors when I run the script: -------------------------------- parse features -------------------------------- => GFF version parser used: 2 [Fri Aug 6 17:34:01...

I got it to run by manually editing the exonerate output, but the output from agat_sp_load_function_from_protein_align.pl was incorrect. Agat reported "no protein aligned" for all genes, but in my exonerate...

Could you share a few lines of a Maker-produced exonerate file so I can compare? Sara On Mon, Aug 9, 2021 at 6:51 AM Jacques Dainat ***@***.***> wrote: > When...

So looking through Maker it is clear that a lot of post-processing is applied to the exonerate output, see /maker-3.01.03/lib/Widget/exonerate/ protein2genome.pm. Do you have any interest in modifying agat_sp_load_function_from_protein_align so...

Here is my exonerate command: exonerate --model protein2genome --softmasktarget --showalignment no --showtargetgff yes --score 500 --percent 70 --bestn 10 --query testSet_insectProts.fasta --target scaffold2.fasta > insectProts2scaffold2.gff The files are attached! insectProts2scaffold2.gff...

I have updated the example files and shared them here: https://drive.google.com/drive/folders/1QlgX2Zp06Ugk6HCoiddYP82xbvdAMz1Y?usp=sharing My exonerate command: exonerate --model protein2genome --showvulgar yes --showquerygff no --softmasktarget \ --showalignment no --showtargetgff --score 300 --percent 50...