User: andres.firrincieli

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Posts by andres.firrincieli

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Comment: C: What is the difference between Average Nucleotide Identity (ANI) and blastn anal
... > Now, I need to know specifically which are strains shared more genes > among them in the accessory gene cluster. Why don't you run a cluster analysis on the `accessory gene cluster frequency table (binary matrix 1,0 aka presence,absence)` to find which strains share a similar `accessory p ...
written 2 days ago by andres.firrincieli1.1k
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Comment: C: scale free topology in WGCNA
... because that is the automatic one-step network construction tutorial. Instead, look at the [step-by-step tutorial][1] if you want to understand how wgcna works. [Here][2] the description of the `blockwiseModules` function [1]: https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/ ...
written 5 days ago by andres.firrincieli1.1k
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Answer: A: scale free topology in WGCNA
... Hello, 153 samples and power of 18 for an `unsigned` network is too high. There is a very nice explanation about power selection [here][1] and [here][2]. In your case I would pick 9. > Third: what is the difference between networktype and TOMtype in > blockwiseModules function?. To constru ...
written 6 days ago by andres.firrincieli1.1k
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Comment: C: Confusion about WGCNA results
... the dissimilarity is quite low. My suggestion is to merge the modules whose expression profile is very similar ([2.b.5][1]) [1]: https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/Tutorials/FemaleLiver-02-networkConstr-man.pdf ...
written 24 days ago by andres.firrincieli1.1k
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Comment: C: Confusion about WGCNA results
... See my answer [here][1] Since the clustering algorithm is not perfect, my guess is that the hub of the `grey` module could actually belong to the `yellow` module. How many genes do you have in the `grey` module? What is the output of `1-cor(MEs)`? [1]: https://www.biostars.org/p/463404/ ...
written 25 days ago by andres.firrincieli1.1k
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Answer: A: Confusion about WGCNA results
... By default the function `plotEigengeneNetworks` exclude the `grey` module which include `non-module` genes ...
written 26 days ago by andres.firrincieli1.1k
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Comment: C: quality control (ribo-seq)
... Hi Andreia, I never worked with ribo-seq data but did you check if those 'weird' plots are caused by some contamination from reads mapping to rRNA ...
written 6 weeks ago by andres.firrincieli1.1k
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Comment: C: WGCNA: Problem with selecting soft threshold?
... Glad it works now. From [WGCNA faq][1]: > If the scale-free topology fit index fails to reach values above 0.8 > for reasonable powers (less than 15 for unsigned or signed hybrid > networks, and less than 30 for signed networks) and the mean > connectivity remains relatively high (in th ...
written 6 weeks ago by andres.firrincieli1.1k
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Answer: A: WGCNA: Problem with selecting soft threshold?
... > ... and used the log normalized count for only diff > expressed genes with is 2065 genes From [WGCNA faq][1]: > First, the user should ensure that variables (probesets, genes etc.) > have not been filtered by differential expression with respect to a > sample trait. See item 2 abo ...
written 6 weeks ago by andres.firrincieli1.1k
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Answer: C: Hybrid assembly to produce full genome
... > The PacBio data was assembly by the sequencing company and yielded 3 polished contigs. I also requested the the raw data for the PacBio assembly so it is available. My experience in bioinformatics is limited and I am not entirely sure how I would go about to obtain a full (circular) genome from ...
written 7 weeks ago by andres.firrincieli1.1k

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Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: WGCNA gene clusters vs eigengenes
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