Alexandra Lee DNAnexus Team
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Recent activity by Alexandra Lee
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Are you asking about how to run REGENIE across multiple phenotypes? Using the current version of regenie within swiss-army-knife, I think you can use the `phenoColList` or `phenoExcludeList` if you...
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Hi Rosemary, Unfortunately it appears that `umount` doesn't work in the terminal in RStudio, as you've found. Thank you for bringing this to our attention - we will make a note of this and work to ...
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Something like `dx extract_dataset` should work. While dx extract_dataset doesn't require using a spark node, depending on the size of the data/number of fields you may need to use a spark node htt...
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As Racheal mentioned, you used entity title instead of entity name when you tried to extract the data which is why our original approach didn't work. To see the list of entity names and titles you ...
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Here are the steps I followed: 1. Launched JuypterLab instance with the following configuration: Cluster Configuration: Single modeInstance Type: mem1_ssd1_v2_x36Feature: PYTHON_R 2. In python not...
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@Alex Shemy? I was also not able to reproduce your error if I run the notebook from top to bottom. However, I get the same error if the `control_dictionary.csv` file already exists and I re-run the...
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To clarify, I am thinking that `local CLI` refers to downloading files from the UKB RAP and running a local instance of the tool on your local machine, so not using the tool instance in the RAP lib...
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Personally I'm not very familiar with the metabolomics data. I believe that only NPX data will be released. However, there is only minimal pre-processing between the raw NGS counts and the NPX val...
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This preprint details (in the supplementary material) the QC that was performed on the data: https://www.biorxiv.org/content/10.1101/2022.06.17.496443v1.full.pdf However, the existing QC and filter...
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Adding this here as an additional resource.: This training webinar walks through how to concatenate regenie results to use with the Locus zoom app: https://www.youtube.com/watch?v=bKiBk4UtbY0&list=...
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