-
Hi,
While loading the results to Trinotate SQLite database, I am encountering the following error:
Error: column transcript_id is not unique
Error, cmd: echo "pragma journal_mode=memory;
pragm…
-
Can someone tell me which assumption convert_gff3_to_ncbi_tbl makes on the formatting of the names? Apparently ours miss something:
```
python3 gff/convert_gff3_to_ncbi_tbl.py -i ../juncus.fasta.…
-
Hi,
After I ran the EVM, I found that there were too many gene structures (nearly 140,000, using the command "cut -f 1-5 EVM.all.gff3|grep'gene'|sort -u" and the remaining 70,000 genes, species The n…
-
Hi everyone,
I am trying to analyze some transcriptome assembly I created via Trinity. Considering the final nucleotide sequence is called .cds, does transcdecoder exclude introns? Because I am loo…
-
Hi!
I'm new to Trinotate and I'm trying to get Trinotate v4 working on our HPC cluster. I used Singularity to initiate the SQLite db and the initial import of transcriptome and protein data. I thi…
-
Hi, I got the error in the end of this message when I ran RunAnnotate.sh
I tried with two different RNA-seq data but ended up with same errors.
Thanks,
Yong
CMD: Trinotate/Trinotate-3.0.2/util/t…
-
Hi there,
I have a quick question about the usage of Trinotate-implemented diamond blasting against supported databases, ie the command Trinotate --db --CPU --transcript_fasta --transdecoder_pep…
-
If doing non-strand-specific RNA-Seq, Trinity will return transcripts in a random orientation. E.g., a given transcript could have a (+) direction coding orf (sense transcript), or have a (-) directi…
-
Hi Brian,
I am using PASA to annotate a genome assembly following the PASA tutorial. The genome is ~500 MB and resulted in 400 contigs. EVM ran successfully and outputted 33k genes (with evidence f…
-
Hi Brian,
When I import data into sqlite, it gives error:
`Error, cmd: /home/data/t120347/software/Trinotate/util/trinotateSeqLoader/TrinotateSeqLoader.pl --sqlite Trinotate.sqlite --gene_trans_map …