Alexandra Lee DNAnexus Team
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Recent activity by Alexandra Lee
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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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I'm not able to reproduce the timeout error based on the code provided. Do you know which command call within this code block is throwing the error? Here is a previous post about troubleshooting Ha...
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I believe you can create a script to use `dx download <filename.cel>` from the terminal. Or alternatively, when you are logged into the UKB RAP, if you navigate to the `Bulk/Genotype Results/CEL fi...
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Just to add to Rachael's already very helpful comments. You can probably follow the steps for extracting proteomics data seen here: https://github.com/dnanexus/UKB_RAP/blob/main/proteomics/0_extrac...
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Doing some more digging, it looks like due to how the ports are setup on RAP that you currently cannot run Tensorboard inside the jupyter notebook notebook. However, internally we're looking into p...
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