Adding NIL sequence data to lab site

This section is for adding genomic sequencing data (.tsv files) onto the existing dataset provided and displayed on the NILs browser page on Andersenlab.org.

Basic Commands To Know Prior

You should freshen up on the following terminal commands.

  • cd - change directories
  • rm - delete files
  • cp - make a copy
  • git

Your Sequencing Data

You will use the gt_hmm_fill.tsv file output from the nil-ril-nf pipeline for this step.

Important

In order for your sequencing data to be properly added, it is important to make sure that there are no empty/additional lines located at the bottom of your .tsv file.

What you do not want What you do not want

What you do want What you do want

Once your file has no empty lines at the bottom, save the file and move onto the next instructions below.

Step By Step Instructions

  1. Clone the andersenlab.org repo
git clone https://github.com/AndersenLab/andersenlab.github.io.git

  1. [Optional] Create a new branch. This is a good idea if you are newer to github and want to make sure you don't break the lab website by doing something weird.

  2. Add your .tsv file into the pages folder of your Andersenlab github directory.

  3. Open terminal and use the cdcommand to change directories into the pages folder in your Andersenlab github directory. If you did everything correctly, when you type ls into your terminal, it should look something like this.

What your terminal should look like

  1. Then run the following commands in your terminal (while still in your pages directory): 
# create a new file called 'copy.tsv' with your data
cp yourFileName.tsv copy.tsv

# run python script which will add your data to full dataset
python addDataTogt_hmm.tsv.py
  1. After running the above commands, your sequencing data has now been added to the existing NILs dataset on Andersenlab.org. You can now remove your .tsv from the pages directory by using the rm command in your terminal. 
rm yourFileName.tsv

  1. Finally, commit your changes and push your code to update the Andersenlab github.

  2. [Optional] If you created a new branch, you need to merge this new branch back into the master branch for changes to take effect.

Viewing your results

Once all changes are pushed, you should be able to view your NIL genotypes in the NIL browser shiny app.