User: andres.firrincieli

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Posts by andres.firrincieli

<prev • 35 results • page 1 of 4 • next >
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Comment: C: How to distinguish between 16S chloroplast reads and real bacteria ones?
... Hi, Unfortunately our samples were processed by the Joint Genome Institute (JGI), so I know very little about the library preparation methodology. I am the guy who processed the raw data. If you give me some time I can tell you how many reads per samples were assigned to chloroplast and mitochondria ...
written 4 hours ago by andres.firrincieli210
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Answer: A: How to distinguish between 16S chloroplast reads and real bacteria ones?
... Hi Light, we used the method described [here][1] to lower the 16S contamination from chloroplast and mithocondria [1]: https://www.ncbi.nlm.nih.gov/pubmed/23995388?dopt=Abstract ...
written 1 day ago by andres.firrincieli210
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Comment: C: Effect of gene size on WGCNA
... That sounds more like a normalization problem rather than how wgcna works. In my experience, in a transcripts network analysis, I found slightly different results, introduced by the normalization, at the level of small modules, but not for the largest ones. If the analysis does not take too long, ju ...
written 13 days ago by andres.firrincieli210
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Answer: C: Linking bacterial taxonomy to predicted genes with Prokka
... Prokka should give you a gff where you can find the association between the contig and its CDS. You could use that file to rename the header of your CDS ...
written 14 days ago by andres.firrincieli210
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Answer: C: Threshold in WGCNA
... > The adjacency matrix in step 2 gives for the weight for each edge. At > this stage how does it select which edges to retain in the final > network? In WGCNA you do not select which edges must be retained in the final network. However, when you raise the correlation matrix to power β you ...
written 15 days ago by andres.firrincieli210
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Comment: C: Identify OTU to species by using MOTHUR
... Just my personal opinion; you are choosing a database based on a feature that is completely useless in regard to the 16S rDNA analysis. Also, keep in mind that greengene is no longer supported since 2013. ...
written 23 days ago by andres.firrincieli210
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Comment: C: Identify OTU to species by using MOTHUR
... With just one phylogenetic marker (16S rDNA) is very hard to classify down to specie level. This has nothing to do with the databases SILVA/greengene or the pipeline QIIME/Mothur. ...
written 25 days ago by andres.firrincieli210
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Comment: C: DADA2/R Programmer Needed for One-Time Job
... True. I had this problem with a microbial community rich in enterobacteriace. ...
written 4 weeks ago by andres.firrincieli210
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Comment: C: constructing network by WGCNA and validation Hub genes
... At this point I would experimentally validate my hub genes. Perhaps only those genes that might have a role in the trait of interest that significantly correlate with your module. Check the literature. ...
written 5 weeks ago by andres.firrincieli210
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Comment: C: constructing network by WGCNA and validation Hub genes
... I could be wrong but, supposing your network is scale free, or approximate to a scale free topology, and you already did the module preservation analysis, does the green module in the Ref. network results preserved in the validation network? If the answer is yes, then you can assume that the hub gen ...
written 5 weeks ago by andres.firrincieli210

Latest awards to andres.firrincieli

Scholar 10 weeks ago, created an answer that has been accepted. For A: Why does my TOM network heatmap for WGCNA display red background and golden modu
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Why does my TOM network heatmap for WGCNA display red background and golden modu
Scholar 10 weeks ago, created an answer that has been accepted. For A: Why does my TOM network heatmap for WGCNA display red background and golden modu
Scholar 3 months ago, created an answer that has been accepted. For A: Why does my TOM network heatmap for WGCNA display red background and golden modu
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Why does my TOM network heatmap for WGCNA display red background and golden modu

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