diff options
| author | zsloan | 2021-10-12 18:56:34 +0000 |
|---|---|---|
| committer | zsloan | 2021-10-12 18:56:34 +0000 |
| commit | 0f396f4a1a753d449cf2975fc425d587d9350689 (patch) | |
| tree | c9dac243dc05e5cb90ccb7f1d96fd599986bf60a /README.md | |
| parent | 976660ce9ef915426c7ce5ff9077b439e4102a2c (diff) | |
| parent | 77c274b79c3ec01de60e90db3299763cb58f715b (diff) | |
| download | genenetwork3-0f396f4a1a753d449cf2975fc425d587d9350689.tar.gz | |
Merge branch 'main' of https://github.com/genenetwork/genenetwork3 into feature/add_rqtl_pairscan
Diffstat (limited to 'README.md')
| -rw-r--r-- | README.md | 40 |
1 files changed, 38 insertions, 2 deletions
@@ -24,7 +24,7 @@ guix environment --load=guix.scm Also, make sure you have the [guix-bioinformatics](https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics) channel set up. ```bash -env GUIX_PACKAGE_PATH=~/guix-bioinformatics/ ~/.config/guix/current/bin/guix environment --load=guix.scm +env GUIX_PACKAGE_PATH=~/guix-bioinformatics/ ~/.config/guix/current/bin/guix environment --expose=$HOME/genotype_files/ --load=guix.scm python3 import redis ``` @@ -32,7 +32,7 @@ python3 #### Run a Guix container ``` -env GUIX_PACKAGE_PATH=~/guix-bioinformatics/ ~/.config/guix/current/bin/guix environment -C --network --load=guix.scm +env GUIX_PACKAGE_PATH=~/guix-bioinformatics/ ~/.config/guix/current/bin/guix environment -C --network --expose=$HOME/genotype_files/ --load=guix.scm ``` @@ -157,3 +157,39 @@ guix. To freeze dependencies: pip freeze --path venv/lib/python3.8/site-packages > requirements.txt ``` + +## Genotype Files + +You can get the genotype files from http://ipfs.genenetwork.org/ipfs/QmXQy3DAUWJuYxubLHLkPMNCEVq1oV7844xWG2d1GSPFPL and save them on your host machine at, say `$HOME/genotype_files` with something like: + +```bash +$ mkdir -p $HOME/genotype_files +$ cd $HOME/genotype_files +$ yes | 7z x genotype_files.tar.7z +$ tar xf genotype_files.tar +``` + +The `genotype_files.tar.7z` file seems to only contain the **BXD.geno** genotype file. + +## QTLReaper (rust-qtlreaper) and Trait Files + +To run QTL computations, this system makes use of the [rust-qtlreaper](https://github.com/chfi/rust-qtlreaper.git) utility. + +To do this, the system needs to export the trait data into a tab-separated file, that can then be passed to the utility using the `--traits` option. For more information about the available options, please [see the rust-qtlreaper](https://github.com/chfi/rust-qtlreaper.git) repository. + +### Traits File Format + +The traits file begins with a header row/line with the column headers. The first column in the file has the header **"Trait"**. Every other column has a header for one of the strains in consideration. + +Under the **"Trait"** column, the traits are numbered from **T1** to **T<n>** where **<n>** is the count of the total number of traits in consideration. + +As an example, you could end up with a trait file like the following: + +```txt +Trait BXD27 BXD32 DBA/2J BXD21 ... +T1 10.5735 9.27408 9.48255 9.18253 ... +T2 6.4471 6.7191 5.98015 6.68051 ... +... +``` + +It is very important that the column header names for the strains correspond to the genotype file used. |