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We need to have an ORF finder for the transcriptome that is flexible to non-AUG start codons. Ideally this would also output ORFs in a gff format testable by extending `check_gff_fasta.py`
Similar …
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we could also consider HMM, SNP calling, ORF finder, finding repeats, GC content, and some k-mer stuff
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Hi Martin,
Hope all is well! I just noticed on my Mac setup that versions v0.9.8 and v0.9.10 reports the following and exists:
```
gecco run -o /Users/raufs/Coding_Projects/test_lsapan/test_pan…
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Hi, great job of binning.
Recently when I use Semibin2 to do the scaffolds binnning, a problem occurred in some samples. The first line is my command. Could you please help me to solve that? Thanks…
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I was working with Finder and I am glad to report that the run completed without any errors for the dataset I was working with. I noticed that for some genes, the CDS was detected properly. There was …
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Hello!
Great project.
It appeared to be interesting for me to ask your opinion on current ORF reconstruction tools. You have chosen the Transdecoder. Are there shortcomings that are expected to appe…
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CC @camilogarciabotero, ref. #297
How would a user go about findings ORFs with BioSequences? To do this, they need to be able to do several fundamental operations that BioSequences currently doesn…
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My goal is to create a genome guided transcriptome assembly using Stringtie and use gffread to convert the output GFT into a GFF3. I seem to be able to create the .gff3 file without a problem, but I w…
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Hi,
I am having problems running the Repeats filter on some highly repetitive genomes. Reference NC_009488.1 dies early on:
```
baga_cli.py Repeats -g NC_009488.1 --find
Traceback (most recent call l…
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Hello,
I am trying to extract coding FASTA from the genome-based transcripts.gff3 file obtained after adding blastp and pfam information. It seems like it adding a line with long characters gtf file …