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Questions about microbial 16s rRNA phylogenetic, ANI Taxonomy, and GGDC

I do understand that you are working with is an isolate and thus what occurs in metagenomics you feel is over doing it, particularly if 16S is e.g. >99% similarity via Blast. Before reading ...
M__'s user avatar
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2 votes

Co-occurrence networks in Metagenomics studies

To answer your question more formally. I strongly believe you are treating the mice with something that will shift its microbial flora. Clearly the experiment is not described. Thus what I simply feel ...
M__'s user avatar
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2 votes
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Variation in 16S rRNA between assemblers - how do I know which is real?

This is easy @Laura - I'm a bit surprised by the results Spades meta didn't have a good reputation, but the criteria assessed was not what you are looking for. Anyway take all outputs and place them ...
M__'s user avatar
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1 vote
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Using average of sequence similarities when delimiting genera - how to deal with outliers?

The basic question is where do genera start and stop within phylogenetics and the 16S 5% rule? This is not a trivial question within molecular taxonomy, especially for bacteria. The key is to define ...
M__'s user avatar
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1 vote
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How do i search by these gene properties in NCBI's GenBank?

This can be done using the NCBI eutils command-line tools. For taxa, the correct incantation for the search string is txid<taxID>[Organism] (assuming you want ...
gringer's user avatar
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1 vote

WCGNA - Relate modules with Y features when the % of variance explained of each eigengen is low

Part 1 Just to clarify on the specific issue of using PC1 alone given the reported result ... Without knowing the underlying ecology, which is important, 30% is too low to any draw conclusions in PCA-...
M__'s user avatar
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1 vote

maxEE parameter from DADA2 package in R

The previous paragraph in the tutorial provides a link to the paper. We’ll use standard filtering parameters: maxN=0 (DADA2 requires no Ns), truncQ=2, rm.phix=TRUE and maxEE=2. The maxEE parameter ...
bodington's user avatar

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