All materials (except software) for the Track 2 Advanced Functional Genomics session in the Genomics for Animal Sciences – Summer Workshop host by NRSP8 and the USDA-NIFA Animal Genomics Collective RCN in Madison, WI in July 2026. https://www.asas.org/meetings/annual-2026/draft-schedule-of-events-and-scientific-program
Please note, this is not a formal GitHub repository that you would download, but itstead is serving as a place to organize and share information in a simple way. If you are participating in the tutorial, there are 2 files on this page that you should download: PPTX slides and data/ scripts. A course agenda is provided as a 3rd file to download if you have not received it previously. The steps below are how to get started in preparing for this workshop following the instructions also sent to participants via email.
Individual files for today are now available here to ensure they are smaller and easier to download on the conference center internet network. https://iastate.box.com/s/6rvouk61xey004m8x4pe112ojx5mmjf8
For the afternoon session PLEASE ONLY download the 04_integration.tar.gz file. You may download the other files later to work with at home. Please note, these files are the SAME as those in the data file provided below in Step 2. If you already have those files, you can access the data there.
To use these files on your machine, you will need to open your terminal software on your laptop. In the terminal software, enter this code
tar xzvf 04_integration.tar.gz
Then you will have access to the files you need. We will NOT do the ATACseq/ChIPseq pipeline due to internet problems. All of the code and instructions you need to run this tutorial are provided in your HPC folder as described below and in the slides. Please try these later today in your hotel.
If you are using NSF ACCESS computing for tutorials, please sign up for an account here: https://operations.access-ci.org/identity/new-user After you receive an account, send it to the course coordinator and after your account is active (you will receive an email to create a password), make sure you are able to login on the HPC resource (see the course reference PPTX slides above).
Download Data and Code used in Workshop: https://iastate.box.com/s/1jcek1gwvcrrxwmdxacodlo5w92dkcvm Please note: you should not have to place these data on the HPC. Once you are logged into the HPC account on Bridges2, the data is located in storage on the Ocean server here: /ocean/projects/bio260049p/shared More information on the file contents and how to navigate these folders is provided below.
Download reference slides to follow the tutorial here: https://github.com/jekoltes/Track2-workshop/commit/90661248ecae7cd631de3f9f35f37282695d30ad
Make sure you have installed the required software onto your laptop based on the guidance provided: https://github.com/jekoltes/Track2-workshop/commit/85bd5feaea27a9ec95caeac56a86634d7c8460e7 Additional sofware used in the HPC section of the course are also listed in this document if you do not have access to HPC resources.
Background information on the new Ensembl-beta web browswer (replacing the current browser in August 2026)
Website: https://beta.ensembl.org/
Tutorial Video: https://www.youtube.com/watch?v=K7cmwK1ODnc
Tutorial Slides:https://drive.google.com/file/d/1j1_sbkULCDnlpaeW6jhaDFpdcdt59jHd/view
Note, additional information is provided in the course PPTX presentation file.
Please find a Word document with the general agenda of topics covered in the workshop here: https://github.com/jekoltes/Track2-workshop/commit/f35f5f10328610907ee8091dc1cd906015e30d10.
Once logged into Bridges2, follow the commands in steps 1 and 2 below to find the data folders. Below these commands are a description of the files within each folder as well as paths you can copy and paste on class day to help you more quickly navigate to the data during the in-class tutorials.
cd /ocean/projects/bio260049p/shared
Note: If the data folder is still as a .tar.gz, you will need to uncompress it like this:
tar -xzvf workshop.tar.gz
cd ASAS_workshop/data/workshop
At this step, you should now see the following when you use the ls command: [userName@bridges2-login012 workshop]$ ls 01_ftp 02_biomaRt 03_api 04_integration 05_atac
The numbers above correspond to the session order in the class. We will start with 1 and move our way to folder 5 through the day. Here is some helpful information about these folders.
/ocean/projects/bio260049p/shared/ASAS_workshop/data/workshop/01_ftp
/ocean/projects/bio260049p/shared/ASAS_workshop/data/workshop/02_biomaRt
Contains 2 files: biomaRt_script.R example_result.tsv
/ocean/projects/bio260049p/shared/ASAS_workshop/data/workshop/03_api
Contains 3 files: api_script.R example_result.tsv sus_scrofa_regulatory_features_rest_api.tsv
/ocean/projects/bio260049p/shared/ASAS_workshop/data/workshop/04_integration
Contains 2 folders: 01_vep 02_integ_example
/ocean/projects/bio260049p/shared/ASAS_workshop/data/workshop/04_integration/01_vep 1- contains 7 files: sus_scrofa_1000_2.vep sus_scrofa_1000.vcf sus_scrofa_1000.vep.vcf_summary.html vep_workshop.sh sus_scrofa_1000_2.vep_summary.html sus_scrofa_1000.vep.vcf sus_scrofa.vcf
# /ocean/projects/bio260049p/shared/ASAS_workshop/data/workshop/04_integration/02_integ_example
2- contains 4 files:
Animal_QTLdb_release59_pigSS11.bed
chr15_longissimus_depth_QTL_cCRE_summary.tsv
Animal_QTLdb_release59_pigSS11.gff
chr7_longissimus_depth_QTL_cCRE_summary.tsv
/ocean/projects/bio260049p/shared/ASAS_workshop/data/workshop/05_atac/
Contains 16 items: 8 files + 8 folders
Files = shell scripts:
xx-02-JOB-trim.sh
xx-05-JOB-rem.sh
xx-08-JOB-filt.sh
xx-10-JOB-peak.sh
xx-01-JOB-qc.sh
xx-04-JOB-sort.sh
xx-07-JOB-dedup.sh
xx-10-JOB-peak-fulldata.sh
Folders within 05_atac/:
/ocean/projects/bio260049p/shared/ASAS_workshop/data/workshop/05_atac/00_ref
/ocean/projects/bio260049p/shared/ASAS_workshop/data/workshop/05_atac/01_raw_data
/ocean/projects/bio260049p/shared/ASAS_workshop/data/workshop/05_atac/03_trimmed
/ocean/projects/bio260049p/shared/ASAS_workshop/data/workshop/05_atac/04_mapping
/ocean/projects/bio260049p/shared/ASAS_workshop/data/workshop/05_atac/06_no_mt
/ocean/projects/bio260049p/shared/ASAS_workshop/data/workshop/05_atac/07_readgroup
/ocean/projects/bio260049p/shared/ASAS_workshop/data/workshop/05_atac/09_filtered
/ocean/projects/bio260049p/shared/ASAS_workshop/data/workshop/05_atac/10_shifted
There are several different text editors that can be used to alter files. Here I will describe how to update a file using nano.
Job scripts: .sh files (please note, these are sometimes named .job if you prefer for organizational purposes)
To modify a file, for example xx-01-JOB-qc.sh
nano xx-01-JOB-qc.sh
#Here is what the file should look like
#!/bin/bash
#SBATCH --job-name=workshop_JOB
#SBATCH --partition=RM-shared
#SBATCH --account=bio260049p
#SBATCH --time=00:10:00
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --output=02_qc/JOB_workshop_%j.out
#SBATCH --error=02_qc/JOB_workshop_%j.err
set -euo pipefail
cd /jet/home/limb/workshop/05_atac #CHANGE- use your username here where "limb" is listed
module load FastQC
fastqc
01_raw_data/workshop_R1.fastq.gz
01_raw_data/workshop_R2.fastq.gz
-o 02_qc
To save the chages, type: control+x (command to start the proceedure to close the file), control+y (saves file name) type: y At this point, you may change the file name, or hit enter to close and save the file as is without a name change.
Note: you need to be in the folder where the job script (.sh in this tutorial) is located Type
sbatch xx-01-JOB-qc.sh
To ensure the file is running, use this command:
squeue
Better yet, jump to only your job:
squeue -u userName
If you want to actively monitor a short job, you can use this command (note to leave this command, you must type: Ctrl+C)
watch squeue -u userName