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phrokka version: v1.4.1
Python version: Python 3.10.12
Operating System: Computing cluster
```Description```
I have run prodigal-gv on my viral genomes to get the ORFs (it also outputs a genba…
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* phrokka version: v1.2.0
* Python version: Python 3.10.8
* Operating System: Linux
### Description
I was trying to run pharokka, but it crashed due to "IndexError: list index out of range". W…
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With prodigal in single mode without prior training, it is possible to specify different codon tables.
Here with table 4:
`prodigal -i input.fa -o output.out -p single -g 4`
With pyrodigal, I see…
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Hello,
Just curious to know how TAMA ORF seeker identifies sense (+) and antisense (-) ORFs?. Couldn't able to retrieve the same predicted (-) ORFs using other ORF finder. Any suggestions why this m…
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I have been trying to run TransDecoder to identify ORFs in a set of transcripts. However, multiple transcripts keep outputting partial ORFs as their first result (i.e. labeled ".p1"). I have looked at…
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When I run the following sequence through transdecoder, it misses a complete ORF of 204 lengths (looking at the longest_orfs.pep file):
>ENSMUST00000000305_ENSMUSG00000000296
`AAAATGAATTATTTTAATGACT…
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https://mp.weixin.qq.com/s/xqO7Wur2cMLLwRUSgR1yuQ
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Hi, there
I have some full-length pacbio data and want to add the UTR sequence in to the data. I used the Transdecoder to do this work. There were something wrong about the results and I am very c…
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Hit another bug in the output data.
Compare
```py
records = SeqIO.parse(fasta_file, "fasta")
orf_finder = pyrodigal.OrfFinder(meta=True)
predictions = [orf_finder.find_genes(bytes(record.seq)) …
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I've now run phanotate on a large number of phage sequences. Its seems to be producing output in most cases. However for a small subset of sequences, no ORFs are found. These sequences are often >20Kb…