Moderator: Asaf

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Asaf5.3k
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Posts by Asaf

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Comment: C: DESeq2 - Between sample normalization of train/test subsets
... You can have a look at this paper for normalization methods: https://academic.oup.com/bib/article/14/6/671/189645 The raw counts can tell a lot depending on the machine learning you're using. If you take the library depth as an input then, again, depending on the algorithm, you might be okay with r ...
written 7 days ago by Asaf5.3k
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Answer: A: DESeq2 - Between sample normalization of train/test subsets
... I'll answer in reverse order: 3) DESeq doesn't use upper quartile normalization, it uses another, better method. 2) It all depends whether you are using the actual values of gene expression in the ML or just the ranks or relation between them. You might as well not normalize the data then. 1) I w ...
written 7 days ago by Asaf5.3k
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Comment: C: Filtering values for two group separately
... You should probably not filter at all ...
written 7 days ago by Asaf5.3k
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Comment: C: Filtering fpkm values for two group separetly
... A. You won't get a reply when people don't understand what you're asking B. Don't use FPKM ...
written 11 days ago by Asaf5.3k
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Comment: C: WDL: how to use scatter for multiple callers?
... I missed something. WDL can't tell the callers what to output, it only collects their output, if you'll define the vcf as output you could use that file later in the analysis. It is not scatter-gather though, just linear execution. ...
written 11 days ago by Asaf5.3k
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Comment: C: How to evaluate one specie lost or gain the chloroplast in the evolutionary proc
... BayesTraits is the leading software I think: http://www.evolution.rdg.ac.uk/BayesTraitsV3.0.1/BayesTraitsV3.0.1.html You've got GLOOME which is more towards sequences but can be adjusted to binary traits I think: http://gloome.tau.ac.il/ ...
written 11 days ago by Asaf5.3k
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Answer: A: Filter human parasites from taxonomic profiling with Kraken
... I personally think that if you're looking into parasites specifically your better option is to have a protein dataset and diamond blastx your DNA against it. I think that it will yield better results than using k-mer based methods. ...
written 12 days ago by Asaf5.3k
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Answer: A: How to write a Genbank Reference with Biopythons SeqIO?
... The Reference __init__ method doesn't accept arguments, you should set the parameters afterwards: from Bio.SeqFeature import Reference ref = Reference() ref.authors='test' ref.title='Testtest' ...
written 12 days ago by Asaf5.3k
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Answer: A: How to evaluate one specie lost or gain the chloroplast in the evolutionary proc
... To answer your question, you can't conclude anything, you can only give probabilities. You can use software to evaluate the trait of each ancestor, i.e. the probability that it was photosynthetic or not. However, you have to have an evaluation of the gain and loss probabilities and make some assumpt ...
written 12 days ago by Asaf5.3k
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Comment: C: How to evaluate one specie lost or gain the chloroplast in the evolutionary proc
... How to add a figure: https://www.biostars.org/p/309884/ ...
written 12 days ago by Asaf5.3k

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Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Good Example Sequence For Psi-Blast
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