Viewing data in the Integrated Genomics Viewer (IGV)

In these exercises we will use the Integrated Genomics Viewer (IGV). IGV is installed on UPPMAX, but since you would then access it over a network connection, the graphics might be sluggish. We recommend that you download and run IGV locally and download the files that you will look at locally. Alternatively, you can put the files in the webexport folder on uppmax and view them from there. More information about that further down.

If you still want to try to run IGV on UPPMAX, please refer to the Uppmax page for IGV instructions for advice.

Visualising a BED, BAM or GTF file from your local computer

In IGV, select File > Load from File … and navigate to the file of interest. From the file extension, IGV will automatically treat the information in the file accordingly.

Visualizing a BED, BAM or GTF file from a URL

In IGV, select File > Load from URL … A window will pop up and ask you to give the correct URL for the file you want to view. Paste in the URL and the file will be downloaded. From the file extension, IGV will automatically treat the information in the file accordingly.

Visualising a SAM file

If the file you would like to view is in SAM format (file ends with .sam), which is a uncompressed text format, you need to convert it to BAM format (file ends with .bam). A BAM file contains the same information as the SAM file but now it is in a binary compressed format unreadable for a human.

To convert a SAM file to BAM format type:

 samtools view -bS fileName.sam >fileName.bam

Before the visualization, you need to sort it and then build a so-called BAM file index

 samtools sort fileName.bam fileName.sorted
 samtools index fileName.sorted.bam

This is explained in some more detail in the read mapping tutorial.

Then, in IGV, just follow the instruction above for choose File > Load from File … and select the BAM file. If you are running IGV locally and did the mapping on UPPMAX, you will have to download the BAM file and the corresponding index file (.bai) from your work folder to your own computer first.

Going to a locus

In IGV, click the textbox which has the word Go on its right hand side. This textbox will typically contain genomic coordinates for the locus you are presently looking at, but it can also be used to find gene locations. Type a gene name in it and press Enter.