Jacques Dainat
Yes I have looked into details, but I think I will note integrate the Getopt::Long::Descriptive you implemented. The thing is the branch parallel I want to deploy has been restricted...
Hi, It took some time and was quite challenging, but I managed to incorporate most of your suggestions into PR #549. Unfortunately, I wasn’t able to merge your branch directly...
Interesting, thank you for your feedback. This is due to the fact that Bioperl has hard time to read fasta that has single line sequences, when sequences get longer than...
The raw annotation contains isoforms, so the completeness is more accurate with this annotation but people do not like the high value of duplication provided by this approach due to...
"intron/exon"" Features locations are duplicated - consider merging qualifiers, unable to remove it.
Nothing we can do here. The AGAT script is a nasty way to avoid the problem, but cannot solve all cases. The format is correct it is a ENA or...
Good request, I’m aware of the problem. It would request lot of work to go through all scripts (The issue is not only in this one). I do not have...
Available since merge of #549. Quiet is `--verbose 0`
I will add a patch but in this case (Class==) the Class attribute will disappear... indeed, value `=` is forbidden and must be escaped as `%3D`. It is mentioned in...
Hi @maximilianh, thank you for your input. I agree we coud mention that the BED format is not particularly suitable for describing coding sequences (GFF/GFT or genepred format are suitable)....
This is possible. If the genes tend to have numerous exons in your species you will have multiple exons that are 5’UTR and multiples exons that are 3’UTR. Thé UTR...