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Hi,
I have a stringtie output in gff3, but parsing with gff3_validator, it provides me the following output:
Fatal Error: cannot parse ID from entry
Scaffold_2 StringTie exon 38612 …
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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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Hello!
Thank you very much for your contributions and your publicly available data!
I have a question regarding the 11 genomes mentioned in your article. Could you kindly let me know if it is po…
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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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I have tried the bcftools csq command with the attached fasta, and three different gff files (one from ncbi, one ncbi modified to add transcripts, and one from ensembl bacteria). In all cases the gff …
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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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Hello,
I am just using PPanGGOLiN for the first time and am encountering an error:
```
Traceback (most recent call last):
File "/home/matwan/anaconda3/envs/ppanggolin/bin/ppanggolin", line 10,…
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Hi,
I want to convert the Prodigal output to standard GFF3 using the command: convert_prodigal_to_gff3.py -i unit2_new_genome.prodigal.gff -o unit2_new_genome.prodigal.gff3
I obtain this error …
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I'm pulling gff files in from IMG genomes. IMG has the data parsed into gff and fna files already along with some other files. I've mergred the gff and fna files into a single .gff3 file and am using …
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Hello,
I am a undergrad student working with rna-seq data and I use hisat2 in my pipeline but for one of the species I am working with I only have its annotation data in gff3 format and the scripts f…