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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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Google Cloud/BigQuery/Genomics data location

Some of our company's work requires that data in the Cloud be stored in the US. For Google Cloud, I can specify bucket locations to US locations. https://cloud.google.com/storage/docs/bucket-locations But for BigQuery and Google Genomics, there's no…
leontp587
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How to run the latest Docker version of Nextclade on COVID input fasta?

I try to run the following Shell code: sudo docker run -it --rm nextstrain/nextclade:latest nextclade run --dataset-name 'sars-cov-2' - -output-all covid19.fasta # fasta file has the data I want to process Nothing could be processed, changed…
player777
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using awk to print header name and a substring

i try using this code for printing a header of a gene name and then pulling a substring based on its location but it doesn't work >output_file cat input_file | while read row; do echo $row > temp geneName=`awk '{print $1}' tmp` …
Ziv Attia
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TPM for TCGA and GTEX RNA

How do I convert TCGA RNA normalized_count the TPM values as calculated for GTEx. Right now the TPM values on GTEx are dramatically smaller than the values of TCGA. The tables that I am looking at are on BigQuery…
eilalan
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BigQuery with limit 10 or fewer extraction value returns correct results, changing limit or adding extraction return null

The following is an issue with genomic data: I use the following query on the pgp data in big query: http://googlegenomics.readthedocs.io/en/latest/use_cases/discover_public_data/pgp_public_data.html (used one sample id for…
eilalan
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Can't access silver-wall-555.TuteTable.hg19 table anymore

I was able to access silver-wall-555.TuteTable.hg19 on Friday (17th of February), but can't access it since 20th of February. Was it removed from Google BigQuery? Lot's os examples are based on silver-wall-555.TuteTable.hg19.
Tomas
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Google Genomics jobs never ending

We were using Google Genomics ReadGroupSets to store our alignment data (BAM files) and it was running amazingly, until yesterday... Yesterday (08/29/2016) our import jobs (Method: readgroupsets.import) started the "running" status, but until now…
Lucas Taniguti
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How to compress a list of files into a single gzip file using elasticluster, grid-engine-tools, and google cloud

I want to start by thanking you all for your help ahead of time, as this will help clear up a detail left out on the readthedocs.io guide. What I need is to compress several files into a single gzip, however, the guide shows only how to compress a…
Howard Davis
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is it possible to use the discovery module from the Google apiclient in Cloud Datalab?

I have a simple python script that does something like this: from apiclient import discovery from oauth2client.client import GoogleCredentials ggSvc = discovery.build ( 'genomics', 'v1', credentials=credentials ) body = { "readGroupSetIds":…
SheRey
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Google Genomics API

Trying to use Google Genomics, following instructions found here: https://developers.google.com/genomics/ Trying to set up OAuth Client id (Section 4: Authenticate), from the GoogleCloud console, step c tells me: "On the APIs & auth tab, select APIs…
user3537244
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Run of Mutiple fastq files for fastqc analysis

I would run the following code for multiple fastq files in a folder. In a folder I have different fastq files; first I have to read one file and perform the required operations by activating the miniconda , then store results in a separate file.…
Luffy
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T-test comparing multiple columns to other columns

I am relatively new to R and need some help with my data analysis. In the attached table, Master Protein Accession column consists of a list of proteins that are increased or decreased in the cortex(C) under three conditions, i.e., control (C),…
Rizwan
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gcloud beta lifesciences, JSON pipeline-file rather than options

I am trying to run gcloud beta lifesciences because genomics API is deprecated. There have been so many changes, genomics API vs lifesciences API. I ran one of my analysis step in google clooud using beta lifesciences. Here is what I found. (1)…
Namshin Kim
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Additional 500 GB persistent disk attached by default

I am trying to run a workflow on GCP using Nextflow. The problem is, whenever an instance is created to run a process, it has two disks attached. The first boot-disk (default 10GB) and an additional 'google-pipelines-worker' disk (default 500GB).…
DUDANF
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Google DeepVariant pipeline on GRCh37 WGS with exome model not finishing

I have an hg19-aligned BAM that I wish to generate a DeepVariant VCF for. I used samtools to extract the header and ensured that the hg19 reference FASTA index includes the same contigs and locations. My original goal was to run only an exome model…
D.J. Bohm
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