Introduction

Paired-end sequencing allows you to sequence both ends of a fragment. Many aligners can then use the paired-end data to better align reads, especially in cases of repetitive regions.

Viewing paired-end data

You can load paired-end files, such as aligned reads in BAM format, into IGB just like any other data file (see - Loading data).

To enable paired-end visualization, right click on the track or track label and select Show as Paired.

Selecting Show as Paired will change the visualization in several ways:

• Paired reads will be connected by a thin black line
• Data that were separated by strand will be placed on the same strand. So long as Show as Paired is active, the strands cannot be separated.
• Color by Strand will be activated. This option can be disabled within the Annotation tab.
• Arrows depicting the direction of each strand will be enabled. The Arrow checkbox can be disabled within the Annotation tab.

If you want to confirm the status of a read, hover over it to bring up the tooltips, or select the read and click on Selection Info. The paired status of the read can be found at paired read.