# GGG201B Lab: Visual exploration of genomic data with the Integrative Genomics Viewer (IGV)

> About me: Daniela Soto, Ph.D. IGG graduate. Former student of Dr. Megan Dennis. Postdoctoral scholar, UCLA. For questions/comments/etc. email me to [e-mail].

## 1. Why to use interactive genome browsers

Genomic data visualization and exploration is a key aspect of genomics research.

**Q1:** Why is good to visualize and interactively explore genomes?
* Different perspective - a picture is worth a thousand words!
* Check our date - tell if something is wrong
* Integrate a lot of evidence
* Make figures for articles
* See how the data responds to different parameters
* It looks really cool :)

**Q2:** What type of genomic data do you use in your research and need to visualize?
* SNP genotypes hundreds of samples
* Gene annotations

## 2. Tools for visual genome exploration

There are two main tools for the visual exploration of genomes:

* UCSC Genome Browser: https://genome.ucsc.edu/


* Integrative Genome Viewer (IGV): https://igv.org/


> There are many others genome browsers, including Jbrowse and IGB (!).

## 3. IGV vs UCSC

My ratings:

| | UCSC Genome Browser | IGV |
| -------------------- | ------------------- | ------- |
| Online availability | ★★★★★ | ★★★☆☆ |
| Offline availability | ☆☆☆☆☆ | ★★★★★ |
| Reference genomes | ★★★★★ | ★★★★☆ |
| Custom genomes | ★★★☆☆ | ★★★★★ |
| Public resources | ★★★★★ | ★★☆☆☆ |

Both options can visualize:
* Genome assemblies (fasta)
* Gene annotations (gff, gtf)
* Reads mappings (bam)
* WGS, RNA-seq, etc.
* Genomic variants (vcf)
* Genomic regions (bed)

Which one to use? Ultimately, it's up to personal preference.

In this session, we will learn to use IGV.

## 4. Online versus desktop IGV

Where to download the desktop app?
Go to: https://software.broadinstitute.org/software/igv/

However, today we will use the online version.
Go to: https://igv.org/app/

## 5. Exploring the IGV graphic interface

1. Selecting a genome
* Load Hg38 genome
2. Browsing by coordinate
* Go to chr15:32,293,372-33,150,812
* Expand the height of the RefSeq track to 400
* Zoom in to _ARHGAP11A_
* Go directly to _ARHGAP11A_ locus using gene name

> Note that IGV and UCSC use 1-start fully closed coordinate system. This article explains the diffrence between genomic coordinate systems: https://genome-blog.soe.ucsc.edu/blog/2016/12/12/the-ucsc-genome-browser-coordinate-counting-systems/

3. Preloaded tracks
* Go to Tracks > ENCODE signals > ChIP-seq
* Search for H3K27ac in 22Rv1 biosample
* Add one of the tracks
* Remove the track

What are we looking at?
<img src="https://hackmd.io/_uploads/BJrnbBBnp.png" width="400">
_Yashar et al. 2022. Genome Biol._

## 6. Case study 1: Variant calling in _ARHGAP11_ gene family

The Dennis Lab performed targeted PacBio HiFi sequencing of genes _ARHGAP11A_ and _ARHGAP11B_ in a cohort of ~200 individuals to accurately identify genomic variation in these highly identical loci.

**Visualizing alignments files**

1. Download files for PacBio reads mapped to Hg38 from individual HG002:
- bam file: https://bioshare.bioinformatics.ucdavis.edu/bioshare/download/cpqqdfge5lfvovq/dcsoto/GGG201B/ARHGAP11.Hg38.bam
- index: https://bioshare.bioinformatics.ucdavis.edu/bioshare/download/cpqqdfge5lfvovq/dcsoto/GGG201B/ARHGAP11.Hg38.bam.bai

> Important note: For this tutorial, we are loading local files. However, when using the IGV desktop app, files can be loaded from local folders as well as URLs.

2. Upload both bam files simultaneously using Tracks > Local File.

Default nucleotide colors in IGV:

**Visualizing variant files**

We can also visualize the actual variants that were called from these reads.

3. Download the variants in VCF format from here and load them into IGV web:
https://bioshare.bioinformatics.ucdavis.edu/bioshare/download/cpqqdfge5lfvovq/dcsoto/GGG201B/ARHGAP11.Hg38.vcf


## 7. Case study 2 ("homework"): Visualizing your GGG201B files

At home, download IGV desktop and load the genome assembly and gene annotations you have generated in class.

> Hint: To upload your custom genome go to Genomes > Load Genome from File. To visualize gene annotations, draf and drop the GFF file into the IGV browser.

## 8. Additional resources

To learn more visit the IGV web documentation:
https://igvteam.github.io/igv-webapp/

Or the IGV Desktop user guide:
https://software.broadinstitute.org/software/igv/userguide