User: lagartija

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lagartija90
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Posts by lagartija

<prev • 81 results • page 1 of 9 • next >
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Metagenomics - Functional analysis
... 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 ...
metagenomics megan written 18 hours ago by lagartija90
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Comment: C: optimal number of clusters from distance matrix input
... 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 lagartija90
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Comment: C: Problem renaming headers in multi fasta file using certain scripts
... 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 lagartija90
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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 lagartija90
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Comment: C: How to use sed command on multiple files
... sorry : `for i in *.faa ; do sed '/^>/ s/ .*//' $i > result/$i ; done` ...
written 4 weeks ago by lagartija90
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optimal number of clusters from distance matrix input
... 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 ...
R clustering written 4 weeks ago by lagartija90 • updated 4 weeks ago by Kevin Blighe67k
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Answer: A: How to use sed command on multiple files
... 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 lagartija90
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Comment: C: viral metagenomics classification: MINIMUM number of viral reads (cutoff) to con
... 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 lagartija90
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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 lagartija90
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Comment: C: Which bacterial genes are the oldest?
... 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 lagartija90

Latest awards to lagartija

Supporter 18 hours ago, voted at least 25 times.
Popular Question 6 weeks ago, created a question with more than 1,000 views. For How to annotate nodes in Cytoscape

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