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Hi Brian,
After running, I can't find the output file in the current folder, could you tell me why?
Here's what I've been running :
docker run --rm -v`pwd`:`pwd` trinityrnaseq/transdecoder …
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**Are you using the latest release?**
1.8.13
Hi there,
I am using funannotate to convert a gff3 to a .tbl file, then to convert the .tbl file to a .gbk file, and then to spit out the transcript…
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Hello Sir, @brianjohnhaas
can you please help me to fix the code for the assembly prediction? I want to pick only the best ORF (not more then one genes for the
same transcript)
**TransDecoder.Pr…
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Having an issue with the hmmscan part of the run
```
Some tasks failed![dammit.annotate:ERROR]
TaskError - taskid:hmmscan:longest_orfs.pep.x.Pfam-A.hmm[dammit.annotate:ERROR]
Command error: 'cat…
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Here is what the nextflow version is currently outputting in a transXpress_results folder in the working directory of the pipeline execution (using rnaSPAdes as an example):
```
0226_Chattonella_sub…
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Hi there,
I as hoping someone could help me, I a**m trying to initialize my Trinotate sqlite database using this code:**
perl /home/ubuntu/miniconda3/envs/trinotate/bin/Trinotate Trinotate.sqlit…
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Hi there,
I recently asked our HPC cluster to install Pasa. I kept running into the following error:
* [Wed Sep 20 21:24:28 2023] Running CMD: cat ./trinity_combined/trinity_transcripts.fa.clean .…
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Hi!
Firstly thank you for the tool.
I try to use my gffcompare gtf output for my analysis. I have tried "/archive/yildize/alotaibi_lab/human_data/transdecoder/TransDecoder-TransDecoder-v5.5.0/util/g…
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Hi Brian I did following command and it give me following error. All the databases and --gene_trans_map are there in the working directory. How to resolve it?
-bash-4.2$ /usr/local/bin/Trinotat…
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Hi Brian,
This isn't so much an issue as a question about how TransDecoder works. I have received a transcriptome assembled from a combination of short-read and long-read sequencing using rnaSPAdes…