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PHI-base fastas sometimes have some weird characters in them that screw up the parsing of MMSeqs results.
Should add a step to remove or replace non-UTF8 or non-ASCII characters before MMSeqs.
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https://mp.weixin.qq.com/s/HGQo0HTfN1QVZGyT7yXWYQ
ixxmu updated
2 years ago
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Hi there,
I'm trying to put together a functional database (for ease of use) for about 24K pangenomes (gene sets). I carried out emapper and now I have the annotation tables for each gene set. Now …
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Steps:
1. Use `mmseqs search` to generate MSA.
2. Use `mmseqs2 result2msa` to convert the mmseqs2 result to hhsuite compatible database.
3. Use `hhblits` to generate `a3m` format result.
My qu…
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Hi,
I'm using vs code via remote-SSH on a HPC cluster. Python3 is not available per default, but loaded via `module load python3`. Activating virtual environments also works, with `source /path/to/v…
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Task: I am looking for amino acid sequences in a genome (nucleotide level) with mmseqs. Equivalent to tblastn.
in the output of mmseqs (mmseqs convertalis) I get not only the target in the column b…
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It appears my genome is too long for Prodigal. Is there a work around?
Thank you!
Sher
code:
- Run gene prediction using a genome to train Prodigal
emapper.py -m mmseqs --itype genome --gene…
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Hello.
I am following the tutorial on [Integrating AGNOSTOS gene categories into anvi'o projects](https://merenlab.org/2021/05/28/agnostos/#import-agnostos-into-an-anvio) using the example data fr…
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Hi,
Thanks for the wonderful MMseqs2, I run it on my 1k+ sample parallelly on computer cluster, most of samples failed with the following errors, only 20% samples succussed:
/opt/gridengine/defau…
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@EvaFriederike I am not 100% sure yet how to handle the mmseqs2 step.
Currently, everything happens in one process. Here, the `mmseqs.sh` script is called that does the indexing of the db and then…