User: lagartija
lagartija • 90
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Posts by lagartija
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... Hi,
I ran my metagenomes through several tools (IPscan, EggNOG...) and now I wish to integrate and visualize my data for functional annotation and viewing pathways through KEGG for example. Do you know a tool for that ?
MEGAN seems good but I don't know if I don't manage to use it just to visualiz ...
written 18 hours ago by
lagartija • 90
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... Thank you, I think I agree. I only have a distance matrix because I am comparing images pairwise and the first step is to output a distance. ...
written 28 days ago by
lagartija • 90
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... So you have you new headers in a file or you just want your headers to be like
ASV1, ASV2... ? ...
written 4 weeks ago by
lagartija • 90
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Comment:
C: Error when running Metabat 2
... Please send us your command.
This worked for me :
`jgi_summarize_bam_contig_depths --outputDepth output_depth_jgi.txt input.bam`
...
written 4 weeks ago by
lagartija • 90
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... sorry :
`for i in *.faa ; do sed '/^>/ s/ .*//' $i > result/$i ; done` ...
written 4 weeks ago by
lagartija • 90
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... Hi !
I am trying to cluster data on R from a distance matrix. I tried hclust (and cuttree) or pam. The problem is, I don't know how many clusters to ask for.
I know a lot of methods are found to determine the optimal number of clusters and clustering method (mclust, pvclust, fviz_nbclust, optCluste ...
written 4 weeks ago by
lagartija • 90
• updated
4 weeks ago by
Kevin Blighe ♦ 67k
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... if you want to treat all the .faa files of your directory you just do :
`for i in *.faa ;
do
sed '/^>/ s/ .*//' $i > result/$i ;
done` ...
written 4 weeks ago by
lagartija • 90
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... You can use that definition. The problem is that viruses are very diverse so it will give a looooooot of false negatives and a lot of false positives too. Set the threshold quite high to be sure that your annotation is correct and if you want to go deeper you will probably have to assemble and class ...
written 5 weeks ago by
lagartija • 90
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Answer:
A: hmm without realigning
... Hi,
maybe a bit late but can help others. Just replace de gaps by "N"s and the hmm will keep the msa structure :) ...
written 6 weeks ago by
lagartija • 90
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... really complicated question. Molecular clocks on very old and divergent genes would probably be quite wrong (correct me if I am wrong but I think that one of the assumptions of molecular clocks is that mutation rate has not changed in the history of that gene).
Maybe you could start by listing all ...
written 3 months ago by
lagartija • 90
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