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As written in the docs, NEASE only supports SE.MATS.JC.txt
- Question 1: Do we support SE.MATS.JCEC.txt as well?
- Question 2: Should we change the error message if any of the other outputs is used …
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Do we plan to spawn japonicus files equivalent to the pombe CDS coordinates and exon coordinates? If so, can they be put in directories that mirror the pombase placement, i.e.
www.japonicusdb.org/d…
mah11 updated
3 years ago
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Another way we discussed to assess annotation quality is to look at overlapping genes, sense and antisense.
You would expect that similar genomes would have the same rate of these classes, if not, t…
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Hi there,
Is there an example for and ? I failed to run sorf_to_genome.py, and kept giving IndexError at exon linesplit.
Thanks!
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Good afternoon,
It is written that "Minimap2 often misses small exons."
I would like to know what is the size of these small exons, since I couldn't find this information online
Thank you
Beat…
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Hi Vizueta,
Thank you for developing a favorable tool for gene family annotation, but now I have some problems.
Some sequences of this ***_genomic_and_annotated_proteins_trimmed_idseqsclustered.…
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Hello Trent,
Thanks again for creating exon! I was trying out the R package and encountered an error when installing from source. I am using a Macbook Pro with M2 processor running clang version 14…
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hi, I want to draw a gene track using bed12 using bed display stacked, however, it only allow to set UTR region color, can I highlight some exons in the track also? how could I modified my data in be…
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Hi @GermanDemidov,
Thanks for the precious tool and the great documentation on it.
I am considering to use the tool for germline (and eventually mosaic) CNV calling in panels and WES scenarios.
…
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Hi,
I run BRAKER3 to annotate a new reference genome I had assembled. I used proteome from the closest species I found as a training set. BRAKER call was
**braker.pl --gff3 --threads=12 --species=Ve…