User: fredjaya

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fredjaya10
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fredjaya1
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Posts by fredjaya

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Comment: C: recombination and low mutation rate can potentially confound phylogenetic signal
... twitter preferred @fredjaya1 ...
written 19 days ago by fredjaya10
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Comment: C: recombination and low mutation rate can potentially confound phylogenetic signal
... I'm not completely sure! From what i've come across, the most prominent study of recombination in SARS-CoV-2 is the 7th reference in my previous post by Boni et al. (2020). Australia's Transformational Bioinformatics group (CSIRO) appear to be developing a method to detect recombination in SARS-CoV- ...
written 19 days ago by fredjaya10
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Answer: A: recombination and low mutation rate can potentially confound phylogenetic signal
... That's right - a sufficient amount of genetic diveristy is required to differentiate phylogenetic taxa/samples, however, "too much" divergence can also introduce artefacts. One common example is long-branch attraction, when using an outgroup that is too divergent from the assumed "ingroup"[\[1\]][1] ...
written 19 days ago by fredjaya10
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Comment: C: Error Bam File Is Malformed: Premature End Of File Using Gatk Tool Baserecalibra
... Thanks for the tips! Came across an identical issue and used `samtools quickcheck your.bam` to identify malformed files ...
written 5 weeks ago by fredjaya10

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