All Questions
4 questions
0
votes
1
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330
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Blast output file only shows 500 lines -outfmt 6
I had created databases of different sets of metagenome datasets - one with 6 runs, other with 48 runs, another with 100 runs, etc using the accession list for each of these datasets and makeblastdb ...
- 149
3
votes
2
answers
89
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How can I improve or otherwise investigate an unreliable genome tree?
Summary My genome tree doesn't agree with my gene trees and I get the feeling that my genome tree might be wrong, possibly due to long branch attraction, but I don't know how to check/fix it.
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- 1,027
3
votes
1
answer
78
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Phylogenetic tree rooting in shotgun metagenomics
But I have some weeks fighting with this issue about phylogenetic tree building to use in a phyloseq object in order to calculate beta-diversity metrics that takes into account tree distance branches ...
- 41
4
votes
1
answer
120
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Co-occurrence networks in Metagenomics studies
I have recently acquired some 16S metagenomics data, and was wondering if anyone can speak of the potential limitations, challenges as well as advantages to conducting a network-based study on ...
- 910