
Ondrej Klempir DNAnexus Team
Activity overview
Latest activity by Ondrej Klempir
-
You should be able to work with full data using JupyterLab from the very beginning with no need to use Cohort Browser. However, I would recommend to first export relevant columns and maybe apply so...
- View comment
- 1 vote
-
@Anastazie Sedlakova? is on vacation right now. I think she will be able to help here once she is back. Feel free to share with us any new findings you might have in the meantime.
- View comment
- 0 votes
-
For your SAIGE question and mixed model work, actually I would like to ask how you managed to run SAIGE? I am also very interested in running SAIGE and have not yet had much success... For questio...
- View comment
- 0 votes
-
Query of the week #8: Filtering BGEN file and exporting geno data to Pandas df
After a one-week pause (were enjoying public holidays), we are back with Query of the week numero 8. This week we will follow up on Query #7. I read a great discussion below the post and this week ...
- Ondrej Klempir
- 3 followers
- 3 comments
- 0 votes
-
Hi @Gary Burnett?, I made a testing run using a UKB cram file, facing an error: Logic error: Got an uncompressed chunk but it was null., exiting." The job log says, "input_options: --tumor-name tes...
- View comment
- 0 votes
-
Query of the week #7: About linking geno and pheno data
Hello everyone! So far, we have focused primarily on phenotypes in this series, and I did not pay much attention to the question of linking phenotype and genotype data. For that reason, I started t...
- Ondrej Klempir
- 3 followers
- 6 comments
- 0 votes
-
Perfect! Thank you.
- View comment
- 0 votes
-
Hello @Elena Jolkver?, have you received any answer back from UKB? I would be really interested in knowing how to read this data in Python.
- View comment
- 0 votes
-
Hi @Burcu Çevik?, my idea would be to create a tar.gz using just the 5 files mentioned above in this thread, i.e. (.pac, .ann, .amb, .bwt and .sa.). @Gary Burnett?, please, it my thinking correct?
- View comment
- 0 votes
-
Yes, I think it might work. However, I assume this (download to local and then upload to UKB RAP) would be much slower than working on RAP.
- View comment
- 0 votes