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```
conda env create -f environment.yml -n dammit-env
Warning: you have pip-installed dependencies in your environment file, but you do not list pip itself as one of your conda dependencies. Conda …
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Hi there,
I would like to reconstruct model gene to train gene predictors, starting from genome guided and de novo transcriptome.I would like to have confirm if these are the steps to follow:
1.…
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Hi,
so I have now switched the transcript alignment over to Minimap (see #79 ) ahead of the actual PASA pipeline since Gmap/Blat are way to slow for my purposes (vertebrate genome annotation).
…
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I run braker2 with RNA-seq data for a green algae genome with low GC content.
I get the final output with warning:
WARNING: Number of good genes is low (30). Recommended are at least 600 genes
…
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Hi!
I'm trying to use the Trinity best transcript set guide but i've the following errror. Does anyone know what is happening?
```
$ trinity_cdhit_feeder.pl -infile non-rRNA_Trinity.fasta.tran…
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Hi!
I got the error below while I was trying to run Trinotate through autoTrinotate.pl for my Trinity-assembled transcriptome (fasta file). I am a beginner in bioinformatics and coding. I tried fin…
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Hi,
I built a transcriptome using rnaSpades and am trying to annotate it.
Unfortunately, there was an error during the process that popped up:
Command failed: 'cat /home/lalini/igor_projects/t…
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TAMA currently uses identity to Uniprot proteins to select ORFs/CDSs. For genes without a homologue in Uniprot, it would great to be able to incorporate other lines of evidence.
- Use custom refere…
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Hi, I am now working on the annotation about a plant genome ~10 Gb genome size. We sequencd the isoseq sequences with Pacbio Sequal platform, that is the full-length transcripts. I used PASA and thes…
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Hi there,
funannotate seems to use a lot of evidence, but I wasn't able to find specifics on how the evidence is used to tune ab-initio prediction exactly in the docs. For example, what evidence i…