I have now been able to run an online BLAST+ search, and have received some interesting results. Now, I would like to use these results to generate a GFF/GTF file for gene annotation to use in a different pipeline.
However, most guides how to do so seem outdated, as they are only referring to the old blastall software, and not to the online output.
I have downloaded the HitTable as *.csv, but I have no clue as to how to convert it to GTF/GFF format.
The scripts suggested here ( How To Convert Blast Results To Gff ) for instance don't work with the output of the online BLAST+ system. The online BLAST+ system also does not accept output format codes such as "–outfmt 6 " as suggested here: https://mgkit.readthedocs.io/en/0.3.4/scripts/blast2gff.html
Could anyone here help me out?