Jacques Dainat
Following this post in parallel https://www.biostars.org/p/9601455/#9601546 I see two potential issues: AGAT creating mRNA while transcripts is expected And in our case hereI think it is related to multiple values...
To avoid to have mRNA instead of transcript in the output you should avoid converting in "relax" mode that allow all type of feature type in column 3. To avoid...
There are probably two issues. One is the fact that you have multiple value attributes like gene_id "name1" "name2"; I should check that it is really problematic before adding a...
@mschilli87 I can easily add patch to avoid gene_id attribute to have several values but I do need the GFF sample that provided the ``` JAPIVC010000802.1 . gene 525047 606909...
I wanted the fasta to make some test directly with cell ranger. I can share a patch with you that you can try otherwise
@mschilli87 Could you try the code from branch 457 ? And let me know if the error left?
Yes I remove double attributes only for `gene_id` and `transcript_id` as it is the only sensible attributes to get a consistent file. P.S: Merging annotation should merge 2 isoforms in...
In the current code it is saved in `agat_other_gene_id ` and `agat_other_transcript_id` attribute accordingly.
I still don't get how you end up with several values in gene_id and transcript_id, I should definitely fix that if it is AGAT that makes this mistake.
Thank you, this helps a lot. I will see what I can don when I will be back from vacation.