Integrative Genomics Viewer (IGV) Satish C Bhalla, PhD Department of Computer Science and Engineering Johnson C Smith University Charlotte, NC

Integrative Genomics Viewer (IGV) Visualization tool for exploring and analyzing large genome datasets Work with prebuilt genomes or import a genome View a variety of data such as expression data, NGS alignments, microarray, epigenomics, RNA-Seq, genomic annotations etc. Run it locally on your desktop or launch it from the Broad Institute website. Must register for launching or down loading. IGV is a Java application 5/22/2018

Outline Launch or download IGV IGV user interface Main Window Tool Bar Ex. 1- Load a genome and define a region of interest Ex. 2 – Search for Bladder Cancer Gene - DAPK1 Ex. 3 - IGV Tools Ex. 4 - SAMTOOLS 5/22/2018

Launch or Download IGV Launch from Broad Institute website: Go to http://www.broadinstitute.org/software/igv/download The first time you sign on, you will need to register to download IGV. Click on the first launch icon (Launch with 750MB); 750MB is the smallest memory available and is sufficient for most applications. Download IGV Alternatively, you may download IGV zip file and install on your desktop. If you want to install and start IGV from command line (UNIX terminal) you will need the binary distribution. 5/22/2018

Launch or download IGV http://www. broadinstitute 5/22/2018

IGV Main Window (Source: IGV User Guide) 5/22/2018

Tool Bar 5/22/2018

Ex. 1- Load a genome and define a region of interest Load a genome – Arabidopsis thaliana. Select a chromosome – chr 1. Define a region of interest. Display the nucleotide sequence. 5/22/2018

Load a genome sequence Arabidopsis thaliana 5/22/2018

Select Chromosome 1 5/22/2018

Define region of interest Click and drag anywhere on the chromosome; zoom in 5/22/2018

Increase the zoom and display the nucleotide sequence 5/22/2018

Ex. 2 – Search for Bladder Cancer Gene - DAPK1 Load a prebuilt genome – Human hg19. Search for a bladder cancer gene - DAPK1. View the gene sequence. Translate the nucleotide sequence to an amino acid sequence. Copy sequence and save it to your hard drive. 5/22/2018

Load Human Genome - hg19 Click on chr 9 5/22/2018

Chromosome 9 Human Genome - hg19 5/22/2018

Search for a bladder cancer gene – DAPK1 5/22/2018

DAPK1 Gene Sequence 5/22/2018

Gene Sequence Translation 5/22/2018

Ex. 3 IGV Tools Use IGV Tools to sort a file, (use SORT command) create an index file (use index command) create a .tdf file, (use ‘to TDF’ command) 5/22/2018

IGV Tools: sort command Sort dnai1.reads.sam 5/22/2018

IGV Tools: index command create an index on dnai1. reads. sorted IGV Tools: index command create an index on dnai1.reads.sorted.sam Output file: dnai1.reads.sorted.sam.sai 5/22/2018

IGV Tools: ‘toTDF’ command Convert dnai1. reads. sorted IGV Tools: ‘toTDF’ command Convert dnai1.reads.sorted.sam to a binary tiled data file (.tdf) 5/22/2018

Ex. 4 SAMTOOLS Install SAMTOOLS Make SAMTOOLS executable (use make command) Use SAMTOOLS to: Convert SAM file to a BAM file Sort the BAM file (use sort command) Create an index on BAM file (use index command) 5/22/2018

Install SAMTOOLS SAMTOOLS is an open source program. Download latest version of samtools-0.1.19.tar.bz2 (514.5 kB) from sourceforge or samtools website http://sourceforge.net/projects/samtools/files/ Unzip and install. Commands are given on the command line in the UNIX environment. Basic usage: samtools <command> [options] If you happen to be using Windows computer, you may buy a KNOPPIX (LINUX) DVD or download Linux on a cd and make it executable. 5/22/2018

How to make SAMTOOLS executable? Start SAMTOOLS and make it executable with make command Point to SAMTOOLS-0.1.19 in the igvdata directory. Right click > open in terminal make 5/22/2018

Convert a SAM file to a BAM file with SAMTOOLS ./samtools view –b –S dnai1.reads.sam > dnai1_reads.bam (Give the full path name of the input file such as: /media/sdb1/igvdata/ dnai1.reads.sam). Note: You may convert SAM to BAM in Galaxy if you are familiar with it. 5/22/2018

Sort a BAM file In order to create an index BAM file, it needs to be sorted first. ./samtools sort –m 1000000000 dnai1_reads.bam dnai1_reads_sorted.bam Note: Modifier –m indicates the maximum amount of memory that can be used 5/22/2018

Create a BAM index file Create an index file on dnai1_reads.sorted.bam ./samtools index dnai1_reads_sorted.bam dnai1_reads_sorted.sam.sai will be created and saved in the same directory as the input file. 5/22/2018