Jacques Dainat

Thank you for your feedback. I have seen better performance on small files but it is still ~2 times faster on your huge file. I will merge the branch and...

@kokyriakidis `awk+sed` command should be enough to convert your - strand VCF file into + strand VCF file. Do you work with a mixed VCF file? or one that represent...

1st column of the matches.m6 should be mRNA identifiers. I guess it is not your case (You might show file samples to check). The standard workflow will: * first standardize...

You can have a look at the help `agat_sp_extract_sequences.pl -h`, or here https://www.biostars.org/p/9465973/ and here https://agat.readthedocs.io/en/latest/tools/agat_sp_extract_sequences.html Proteins are made of CDS not exons... In short it will be: ``` agat_sp_extract_sequences.pl...

I guess you can process the GTF with AGAT (gxf2gxf script) and it should be standardize to be submitted as a GFF file.

Hi, AGAT is not multithreaded, it is useless to provide more than 1 CPU. (FYI I had plan to update the code to multithread the parsing but I'm do not...

Your command sounds good. Is `uniparc_active.fasta` the db you use to create the matches.m6 file? I had an issue on OSX when they updated the HDD system, the DB created...

> Should the indexed database be kept in the same working directory of agat? No AGAT should index in its own way the fast file.

Hello, First I do not agree, prokaryotes have mRNA. If the mRNA feature is not present, processing the data with `agat_sp_fix_features_locations_duplicated.pl ` to remove the duplicated locations will add the...

Sounds a good task for AGAT. We will think about it.