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Hi there
I'm using PASA for annotation comparisons and annotation updates, but I think that something wrong is occurring
Here are my annotation BUSCO results generated with EvidenceModeler:
Numbe…
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Hi, there
Good AGAT for the analysis for the gtf or gff3 files. I have used the agat_convert_sp_gxf2gxf.pl to add the gene name into the final gffs files ,it works well. After I check the results …
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Hi, I am opening this thread to discuss the role of ORF data in the mikado pipeline.
Mikado tutorial recommends transdecoder to find potential ORFs in the data. The first issue with transdecoder is …
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Hi, Thanks for writing the scripts for Isoseq analyses!
I'm trying to convert all of my gtf file and gff file to bed12 format for tama_merge. But somehow it complains "gene_id" is not found, though…
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Hi,
If I have several RNA data sets (for example, different tissues or biological repeats), so I have 3 options to use these data sets to assemble transcripts,
1) Merge all raw reads and then map …
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I am trying to run convert_gff3_to_ncbi_tbl.py script but getting this error.
```
ubt80:EMBLmyGFF3 arslan$ python3 convert_gff3_to_ncbi_tbl.py -i juncus.fasta.transdecoder.refined.gff3 -o arslan.…
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I am running the following command.
$ braker.pl --species=yourSpecies --cores 8 --genome=/home/Braker/genome.fasta.masked --prot_seq=/home/Braker/Protein_hints.fasta --prg=gth --bam=/home/Braker/RNA…
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Hello-
I am having problems running trinotate. I am on the "Initial import of transcriptome and protein data" step outlined at https://github.com/Trinotate/Trinotate.github.io/wiki/Loading-generate…
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Hi, I have freshly installed funannotate through conda, then removed augustus by using "conda remove --force-remove augustus". After that I locally installed augustus 3.3 through apt-get and redirecte…
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Hello, I am using funannotate update to have a more accurate UTR regions from a model organism using dRNA reads. It seems that does have a problem parsing the GenBank files that funannotate creates:
…