Jacques Dainat
Thank you for reporting this bug. Have in mind that submitting translated CDS is not mandatory. EBI will make and add the translation.
It has been requested see #422 but I need a detailed example (few sam lines and the expected results)
To check hat version you have installed with conda use: `conda list` To check what version is available in conda do: `conda search -c bioconda agat` To install the desired...
Interesting, this test is to deal with empty sequence ID in GXF. I guess this is problem related to the version of bioperl used. To visualise the difference, once you...
Sure, but I would need a detailed example to be sure to implement it properly
Here as level2 feature are different (mRNA vs transcript) everything will be kept, like a cat command. If you change transcript by mRNA then they should be compared. I do...
4. ^^ the gene from addfile.gff will be added to file1. In the merge case, a new transcript isoform will be created and attached to the original gene from file1....
To check the presence of start and stop you can extract the protein with AGAT and then use ‘ gaas_fasta_checkProteins.pl’ from [GAAS](https://github.com/NBISweden/GAAS) But I’m not sure to get what is...
Might be related to CDS phase. Is is taken into account by geneious? Try to extract the record from the gff. Set the phase manually to 0 and run agat...
As seen in other cases, may be due to long one-line fasta sequence. You should fold the fasta sequences before to be sure.