Hands on activity: Beginning computing for genomics
Overview
This is a test of OER commons module sharing. Please reach out to hcbeale@ucsc.edu if you'd like more information.
Define your variables
Modify the variables defined below with the information about your variant found in the google sheet Variants to investigate TUBI 2023. The variables full_variant_id, gene, AA_change, and g_id come from the columns of the same name. chr comes from Chromosome and pos comes from Start_position. your_username is the login you use for ssh.
Commands (change them to match your variant and login)
full_variant_id="NRAS Q61" g_id=G27492 chr=1 pos=115256529 gene=NRAS AA_change=Q61 id_gene_mut=${g_id}_${gene}_${AA_change} your_username=hbeale
Example Results
hbeale@ip-172-31-49-24:~$ full_variant_id="NRAS Q61" hbeale@ip-172-31-49-24:~$ g_id=G27492 hbeale@ip-172-31-49-24:~$ chr=1 hbeale@ip-172-31-49-24:~$ pos=115256529 hbeale@ip-172-31-49-24:~$ gene=NRAS hbeale@ip-172-31-49-24:~$ AA_change=Q61 hbeale@ip-172-31-49-24:~$ id_gene_mut=${g_id}_${gene}_${AA_change} hbeale@ip-172-31-49-24:~$ your_username=hbeale hbeale@ip-172-31-49-24:~$