Former User of DNAx Community_6

Error Reading Public Datasets

Hello, I am trying to access the publicly available gnomAD dataset from AWS s3// file systems but I am getting timeout waiting for connection from pool error. May I know how to proceed with this er...

• 06 February 2023 00:00
• 3 followers
• 8 comments
• 0 votes

I am trying to access the files from MNT/PROJECT but not accessible

Hello, I am trying to use data in /mnt/project and upload it to hail and do the subsequent analysis. Although the results are running well when I did the initial import_plink. I am getting a file n...

• 03 February 2023 00:00
• 2 followers
• 4 comments
• 0 votes

How to upgrade a package in dna nexus?

I am trying to use hail and it's not recognizing data hosed in /mnt/project/, I tried copying the file to  /opt/notebooks/, but I am still getting the file not found error. I am not sure what is th...

• 02 February 2023 00:00
• 1 follower
• 1 comment
• 0 votes

I would like to ask you a question. Is it possible to create an applet to use the tools I installed in my environment and load the applet to use it later for other analysis? if so May I know how to do it?

• 30 January 2023 00:00
• 2 followers
• 2 comments
• 0 votes

I have seen a public resource hosted in google cloud and would like to access that information in DNAnexus. Is it possible to access datasets that are in gs:// from DNAnexus?

• 25 January 2023 00:00
• 3 followers
• 8 comments
• 0 votes

I am having issues starting a jupyter notebook. I could able to see the notebook running in the monitor section but not where we launched the notebook. Can someone help me how to resolve this?

• 18 October 2022 00:00
• 4 followers
• 6 comments
• 0 votes

How the vcf files were formatted and how to process the vcf files.

Hello, I am looking for ways to process the vcf files. I tried processing using the swish alpha knife and took a long time to upload the data to the cloud. I also observed for each chromosome, we h...

• 17 October 2022 00:00
• 1 follower
• 1 comment
• 0 votes

I am looking for NMR metabolites in UKB RAP phenotypes. I have a few questions: 1.) May I know how many NMR metabolites are in UKB RAP? 2.) Can you help how to find all metabolites? 3.) What QC steps generally were followed?

• 14 October 2022 00:00
• 2 followers
• 5 comments
• 0 votes

Hello, I am trying to generate phenotypes with Time to Events for the survival analysis I want to conduct. Did anyone generate these before if so Please do let me know how to do it. Thank you so much for the help..

• 14 October 2022 00:00
• 1 follower
• 3 comments
• 1 vote

I am trying to find WGS vcf files. I see individual-level vcf files per sample. Where can I find joined called vcf files for WGS located? Please do let me know how to access those and use them for the extraction of the gene region I am interested in.?

• 12 October 2022 00:00
• 2 followers
• 8 comments
• 0 votes