User: miles.thorburn

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Posts by miles.thorburn

<prev • 59 results • page 1 of 6 • next >
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Answer: A: Effect of assembly quality on CNV detection
... Well, if anyone else finds this issue, albeit fairly niche considering what I'm doing, the smaller contigs likely affect the discovery of discordant and split reads. My solution at this moment is to try and guide assembly of one reference genome using the other through a synteny analysis. I'm using ...
written 11 days ago by miles.thorburn90
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Effect of assembly quality on CNV detection
... I am working on a project testing the difference between two reference genomes. However, one of the most obvious differences is the level of the assemblies - one is chromosome level, the other is contig level. This doesn't create too much of an issue as I plan to find syntenic blocks, liftover annot ...
lumpy cnv written 16 days ago by miles.thorburn90
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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 3 months 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 3 months 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 3 months ago by miles.thorburn90 • updated 3 months ago by Haci220
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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 6 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 6 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 6 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 6 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 6 months ago by miles.thorburn90

Latest awards to miles.thorburn

Popular Question 9 weeks ago, created a question with more than 1,000 views. For Multiple Sequence Alignment for very large data sets
Popular Question 5 months ago, created a question with more than 1,000 views. For Multiple Sequence Alignment for very large data sets
Scholar 12 months ago, created an answer that has been accepted. For A: Filtering VCFs and Phasing
Scholar 12 months ago, created an answer that has been accepted. For A: Filtering VCFs and Phasing
Scholar 13 months ago, created an answer that has been accepted. For A: Filtering VCFs and Phasing
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Filtering VCFs and Phasing

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