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Hi,
The tool says that it can work with GFF3. But it only works with GTF. Can we get GFF3 support?
![image](https://github.com/user-attachments/assets/53e82137-3291-454e-b21f-762e2639b3d6)
Er…
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Hello!
I have got a de novo genome assembly from Illumina PE sequencing. This assembly has got 8.7 million scaffolds in fasta format. I splitted this fasta file to multiple fasta files. One fasta f…
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Native AUGUSTUS GFF3 format is lacking correct unique ID= field for CDS features (they should have an incremented number for each gene), most other features except gene, transcript and CDS completely …
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Dear all,
I am using RiboDiPA 1.10.0 in R version 4.3.3, and when I run the wrapperFunction (RiboDiPA), it failed in the indexing step:
`Indexing`
`Data/Raw/RiboSeq/IMGN_B17/IMGN_B17_Riboseq_re…
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Hi Josh,
The format of output gff3 file from GALES is incorrect.
For reference here is the link to ["Annotating genomes with gff3"](https://www.ncbi.nlm.nih.gov/genbank/genomes_gff/) from NCBI.
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Hi team,
I just found this tool during my search for a tool fixing my gff file. However, error happens when I am trying to fix CDS phases. Do you have any idea how to mitigate this? Any help would …
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Hi Brian,
I have followed the steps outlined in "https://evidencemodeler.github.io/", however, when I execute the command "convert_EVM_outputs_to_GFF3.pl", this error message pops up:
// Process…
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**1. What were you trying to do?**
I used `vg rna` to build a spliced pangenome and a pantranscriptome with a GFA file from PGGB and a gff3 file. Similarly, I used `vg autoindex` to build index f…
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How can I use this command to merge 3 or more gff files with different formats(like gff3/gff/gbff or gff3.gz/gff3)
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Hi Brian,
When I try to convert a GTF file obtained from gffread to GFF3 using the script "gtf_to_gff3_format.pl", I get the following types of Warnings and Errors on screen. I do not know what is …