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Dear Authors,
thank you very much for providing the pipeline! I would like to run the pipeline on different genomes together to compute whole genome alignment of different species to use them afte…
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Hi,
I'm trying to use trinotate using data from gene prediction produced by Braker2.0 (augustus).
Thank to your help I managed to go through the first step of Transdecoder (https://github.com/Tra…
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Hi,
I ran the command:
parsnp -r ref.fna -d fna_files/*.fna -p 20 -c -x --min-partition-size 40
Portions of the output is below:
(this is the first few lines)
/home/doy.pinili/.conda/envs/par…
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Is it a top-level fasta asset, like the genome fasta? Or, is it a child asset, with parents of a genome fasta and transcritome annotation file? then, it needs its own recipe to create the fasta asset.
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```
What steps will reproduce the problem?
1. choose a FASTA file with long headers as infile.fasta
1. run 'cd-hit -i infile.fasta -o outfile.fasta'
2. run 'cd-hit -i infile.fasta -o outfile2.fasta -d…
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Hello everyone,
After installing InterProScan and placing Phobius, SignalP, and TMHMM in the folders required by InterPro, the following analyses still appear to be disabled:
Deactivated analyse…
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Feature request:
It would be nice if igv.js supported bgzipped fasta files for the "reference" object. (I assume it is not supported, as it is not mentioned [here](https://github.com/igvteam/igv.j…
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IPA produces:
- `*.purged.haplotigs.fasta`
- `*.purged.primary.fasta`
HiFi asm produces:
- `*.bp.hap1.p_ctg.{fasta,gfa}`
- `*.bp.hap2.p_ctg.{fasta,gfa}`
- `*.bp.p_ctg.{fasta,gfa}`
- `*.bp.p_u…
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I am struggling to understand the useful looking `-F` option, which allows one to pass a fasta file from which k-mers are extracted and used as reads. I suspect I have misunderstood the manual:
```…
bede updated
7 months ago
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Hi,
I just want to add a new species as outgroup, like this, so how can I finish this procedure? I saw you said that the halReplaceGenome can add a new hal file as outgroup. But I just have a fasta…