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**Are you using the latest release?**
Yes - 1.8.14
**Describe the bug**
Trying to run funannotate update command with new transcriptomic data to update a pre-existing .gff genome annotation file.…
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The documentation should keep mentions to Taito at a minimum, as this makes it easier to remove all the Taito related stuff once Taito goes away.
Referencing Taito is ok when comparing changes to …
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Hello, brianjohnhaas. I found an little problem when using PASApipeline v5.2 to update my genome annotation.
I install the PASApipeline using the conda. the environment yml file look like this:
…
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We are using TransPi to annotate transcriptome of plants but we also want to retrieve mitochondrial and plastome (chloroplast) genes/sequences from them. Those sequences are present in the assemblies …
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## Describe the issue
Unable to combine --cache and --gff without getting a 'Segmentation fault (core dumped)'. Reducing the buffer size did not help.
## Additional information
I am trying to ann…
rsalz updated
2 years ago
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Hi!
I'm using TransDecoder to identify candidate CDS from a StringTie GTF file. I convert the StringTie GTF file to a GFF3 file and there are about 33,400 genes. I do a quick count on the number o…
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see https://groups.google.com/g/trinityrnaseq-users/c/xrPgUtYt3rQ/m/dl457dQBAwAJ?pli=1
and
https://gitlab.com/ezlab/busco/-/issues/440
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Hello, I recently used STAR v2.7.9a to generate inputs for StringTie and BRAKER for part of the annotation pipeline for a few plant genomes.
With BRAKER, the resulting protein file had ~86% of comp…
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Hi,
I am newly associated with transcriptomics and Trinity. From the paper "https://dx.doi.org/10.1038%2Fnprot.2013.084" i have come to know that Trinity also can assemble the isoforms. For downstrea…
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Hi,
I have 3 gff3 files created by [Transdecoder](https://github.com/TransDecoder/TransDecoder/blob/master/util/cdna_alignment_orf_to_genome_orf.pl). These files were all generated with the same sc…
rsalz updated
3 years ago