Reads Being Obscured By Blue Lines

[Houston Saxe]

Hi,

I'm trying to view smallRNA-seq reads against a region of interest within my reference genome. However, I'm getting blue smears covering up the reads of interest. They might be splice junctions. Is there any way to remove these? I have circled the problem in my screenshot below. Any help is greatly appreciated!

 

[igv-help]

The blue lines connect the different parts of a single aligned read in RNA-seq data - they cannot be disabled. They are the same type of blue line that you see in the other tracks higher up in the IGV window in your screenshot. The difference being that the tracks you have circled are in "Squished" mode, so it compresses each alignment to be very short - the same height as the blue lines. So the blue lines are not covering up any read segments - but it can be hard to see if, for example, there is a single grey alignment in amongst the blue. Right click on the track and select "Expanded" to view these tracks the same as the ones above. Or "Collapsed" to set the height to be in between "Expanded" and "Squished"