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Questions tagged [google-genomics]

Google Genomics provides an API for working with genomic data on Google's infrastructure.

Google Genomics provides an API for working with genomic data on Google's infrastructure. For more information see:

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How much of Google-Genomics is open to those studying other organisms?

I'm wondering how much of the Google Genomics environment is flexible enough for those who do not work on the human genome? I couldn't find an obvious place to answer this question, and would prefer not to get too deep in and then find out its only…
Steve Rounsley
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How to transform column to row in Terminal Linux? But more complex

How I transform column to row in Terminal Linux? But more complex... The following is an example of my data: SNP_Name ID_Animal Allele Chr Position rs01 215 AB 1 100 rs02 …
Amanda Botelho Alvarenga
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Google Genomics API - Internal Server Error + ReferenceIDs

I'm pretty new to Google genomics APIs. I'm trying to create an annotation. I used both web version and Python API call: service.annotations().create(body={ 'annotationSetId': '101', 'name': 'TestAnnotation', 'referenceName': 'chrM', 'start': '1',…
AmirCS
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Does dockstore-tool-samtools-index have GATK/BAM/Chromwell already configured?

Just wanted to know if the docker image with name dockstore-tool-samtools-index which is available here "https://quay.io/repository/cancercollaboratory/dockstore-tool-samtools-index" and given as an input to the Google Genomics API…
Ruturaj Kulkarni
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Specifying Parallel Environment on Google Compute Engine using Elasticluster

I recently created a Grid Engine cluster on Compute Engine using Elasticluster (http://googlegenomics.readthedocs.org/en/latest/use_cases/setup_gridengine_cluster_on_compute_engine/index.html). I was wondering what is the appropriate command to run…
Elyas
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How to add client_secret without using argparser?

I want to test Google Genomics. I have a project and I can run main.py from the getting started with the api. But this files hides under the hood of oauth2client how credentials are generated: import argparse import httplib2 from apiclient.discovery…
llrs
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Google Genomics API Callsets Search "Unknown field name: datasetIds"

I've been using the Google Genomics API for about a day now. I've successfully called many of the APIs like Datasets.list, Datasets.get, and even Readsets.search but I'm having a problem with the Callsets.search. I'm making POST request to: POST…
chrislondon
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How do I intersect two data.frames in R?

I have two tables that are in the data.frame structure. Table 1 contains a column of 200 gene IDs (letters and numbers) and Table 2 contains a list of 4,000 gene IDs (in rows) as well as 20 additional columns. I want to intersect these two tables…
Jordan
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How to run PCA, distance matrix and other math procedures on genome VCF files in R?

I am learning to process VCF (variant call files) to produce plots and reports. Here is the R code, which crashes for unknown to me reasons. Please advise how to fix it and tell appropriate tutorials. library(VariantAnnotation) …
Vassia Alk
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