User: miles.thorburn

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Posts by miles.thorburn

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Comment: C: R: Plotting MSMC/PSMC results using ggplot2
... Thank you. I never realised this type of plot had a specific name. ...
written 16 days ago by miles.thorburn90
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Comment: C: R: Plotting MSMC/PSMC results using ggplot2
... Hi Amar, it's the same data. I've added one population worth of data so you can see for yourself. It's not zooming that I'm after, it's to make the lines less "smoothed" and more abrupt when they go back in time as this is the norm for this type of plot in publications. Among other differences that ...
written 21 days ago by miles.thorburn90
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R: Plotting MSMC/PSMC results using ggplot2
... I have finished my coalescent simulation analysis for all my populations, and now want to plot the results using ggplot, but I don't know how to parameterise it so that it matches the expectations for such a plot type. The above plot is kind of the expectation, but when I use the same parameters in ...
R ggplot msmc written 22 days ago by miles.thorburn90 • updated 21 days ago by Haci170
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Comment: C: Software recommendations for amplicon filtering and genotyping
... I have no idea how common people try to filter reads in the manner I suggest in step 1. But, in case there is anyone that does, I have written an [R script][1] that parses blast+ output tables in the manner I suggest above - albeit a little specialised in my case. [1]: https://github.com/dthorbu ...
written 3 months ago by miles.thorburn90
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Software recommendations for amplicon filtering and genotyping
... In a current project, I am trying to find suitable software for two specific tasks. Our first attempts to process the data has led to an overall number of alleles that is impossible to be real, so we need to impose some stricter filters. Most I can write scripts to perform, or use existing tools. Th ...
genotyping written 3 months ago by miles.thorburn90
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Comment: C: R: Iteratively name output of vectorised function
... Edit: I misunderstood what you wrote. That is a mistake I hadn't caught. Thanks ...
written 3 months ago by miles.thorburn90
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R: Iteratively name output of vectorised function
... I am trying to generate a series of fasta files with the number of sequences replicated by the estimated copy number of said sequence. I have a bunch of populations and using loops would achieve this, and my code currently has a loop at it's core. But I can imagine there is a better and faster way. ...
R written 3 months ago by miles.thorburn90
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Answer: A: How to retrieve all GO terms at level 2 from a list input
... Whilst a little late, I've been looking for something similar and found a way to do it in R. This is an adaptation from the code I found on the bioconductor support forums. This script gets all children of a given GO term, but it wouldn't be difficult to adapt to get ancestral terms instead. To ge ...
written 3 months ago by miles.thorburn90
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Comment: C: Can't pair-end fastqs after filtering
... Yeah, I believe I have my answer. Unfortunately, it means it's back to the square one, and we'll have to find another methods to filter reads. I think we will now have two levels of analysis; a conserved data set, and a broad data set. The latter will be only paired reads that are ~97% (threshold no ...
written 5 months ago by miles.thorburn90
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Comment: C: Can't pair-end fastqs after filtering
... Firstly, the reasoning for the sampling design is explained in the previous post that's been linked twice in this thread. I don't compare reads between R1 and R2s, I compare reads between RXs of the same individual - we used two separate samples per individual to verify alleles are real as we are wo ...
written 5 months ago by miles.thorburn90

Latest awards to miles.thorburn

Popular Question 10 weeks ago, created a question with more than 1,000 views. For Multiple Sequence Alignment for very large data sets
Scholar 8 months ago, created an answer that has been accepted. For A: Filtering VCFs and Phasing
Scholar 9 months ago, created an answer that has been accepted. For A: Filtering VCFs and Phasing
Scholar 10 months ago, created an answer that has been accepted. For A: Filtering VCFs and Phasing
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Filtering VCFs and Phasing

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