Review ChIP-Seq Data using IGV

Integrative Genomics Viewer (IGV) is adopted by many researchers working with next-gen sequencing data due to its speed and capability to handle large data sets. BxChIPSeq provides output files (TDF file for sequence coverage, bed file for peaks) that can be loaded into IGV.

Step 1. Install IGV. Go to IGV website, register for a free account with your email address, and now you can download and install it to your computer. Launch IGV with 750MB will be enough for most users. But if you computer can handle it, launch with more memory to make it run faster.

Step 2. Download the TDF files for sequence coverage files and the bed files for peaks. Save them to a folder you can easily locate. You may need to move the files from the default place where your browser saves files to your destination folder.

Step 3. Launch IGV, select the appropriate genome build (e.g. hg19 or mm9) that matches your data. You can find the genome build information in the webpage for your ChIP-Seq data.

Step 4. Load the TDF and bed files.

Load the TDF and bed files to IGV Brower

Step 5. Adjust display range. We need to make the display range the same for all ChIP and Input tracks.

Open Set Data Range Option in IGV

In the Data Range window, enter 35 as the maximum. The sequence tag count file has been normalized to 10 million tags for all experiments, and we have found that 35 is a good starting point. However, you may want to increase this to 100-200 for very tall peaks, or decrease this number to ~10 to view weak peaks better.

Set Data Range for Sequence Tag Count Tracks

Step 6, now you can enter a genomic range, a gene or gene name in the search box in IGV. For example, for the demo ChIP-Seq experiment data for TCF7L2 transcription factor in HepG2 cell line, you can enter gene name VAV3 to see three strong binding sites at or near this gene.

View ChIP-Seq Data in IGV with Same Data Range for All Tracks

With IGV, you have many options to display your data. Please see the IGV's User Guide for more information.

You can use BxChIPSeq service to quickly turn your raw sequencing data into formats that can be viewed by IGV and other browsers. 

 

Integrative Genomics Viewer (IGV) is adopted by many researchers working with next-gen sequencing data due to its speed and capability to handle large data sets. BxChIPSeq provides output files (TDF file for sequence coverage, bed file for peaks) that can be loaded into IGV.