How to view the sequence of the transparently mapped reads

Question

[wes]

I would like to map the Illumina reads against the assembled genome. There is two regions in the genome with inverted repeat. Therefore, it is expected to observe alignment with transparent border in IGV. According to the link below, it stated that alignments that are displayed with light gray borders and transparent or white fill have a mapping quality equal to zero. The read also maps to another location with equally good placement. https://software.broadinstitute.org/software/igv/AlignmentData

However, may I know how to view the sequence of the reads (transparent) highlight in the box since there is coverage indicated at the top of the bar at the IGV (picture attached)

Answer 1

[GenoMax]

I assume you want to see soft-clipped bases that are not normally displayed by default in IGV. You can show them by changing a preference setting. Go to Tools --> Preferences --> Alignments. Scroll down to find a section called Show soft-clipped bases, toggle it on. Save your preferences. You may need to restart IGV and reload your files.

[wes]

yes, thanks for the guidance and it works!