how to

Transcriptome QGT Lab 2022 Setup

𝕋he instructions in this blog were written to set up the lab in Rstudio cloud […] Linux is the operating system of choice to run bioinformatics software. You will need either a computer running linux or or mac os, which has a linux-like environment. […] #install R packages … Read more →


2022-05-17 Charles Zhou
𝕋his is a workflow to show how to open jupyter notebook on CRI or RCC. There are some detailed instructions here, CRI’s instructions and More general instructions […] […] log into … Read more →

How to convert GTEx v8 model to hg19 based on UK Biobank SNP set mapping

2020-11-23 Sabrina Mi
/gpfs/data/im-lab/nas40t2/Data/References/mappings/UKB2GTEx_mapping.txt.gz contains information for variants in UK Biobank genotypes. The columns are variant chromosome position non_effect_allele effect_allele rsid zscore panel_variant_id 1:692794:CA:C chr1 757414 CA C 1:692794_CA_C 1 NA … Read more →

Working with Large Files

2020-11-23 Sabrina Mi
𝕎hen working with large datasets, only the files with code should be pushed to Github repositories, not the data itself. The raw data inputs or analysis output should either be kept in a local directory that is never committed, or for best practices, they should be stored in Box (download). Once … Read more →

Installing tensorqtl module

2020-11-11 Festus Nyasimi
𝕀nstalling tensorqtl requires pytorch which is based on gpus but there is also a cpu based version. CRI has set up pytorch for cpus as in a conda environment and that is what I am going to use to set up tensorqtl. I will install the tensorqtl in im-lab share space for lab use. […] Create a … Read more →

Querying bgen files in CRI

2020-11-10 Sabrina Mi
𝔸 bgen file has a header block with information about the file, including number of samples, the number of variant data blocks, and flags which describe how data is stores. A variant data block contains data for a single snp, including ID, position, and alleles. bgens from UKBiobank also have a … Read more →