I am quite new to RNA-Seq, hoping someone could guide me here.
I am mapping my sequencing reads against the HIV virus + human genome with a reference genome I made by adding the hiv-1 genome to the hg19 reference genome. Mapping was done using STAR and I wanted to view the chimeric junctions using IGV.
However, when I load the chimeric SAM file into IGV, I could only see the mates mapped to the virus genome and I could not visualize any reads mapped to the human genome. Even selecting view position of mate in the hiv view, it will go to the position on the said chromosome but there is no resulting read seen.
Any suggestion on how can I visualize the chimeric reads?
Thank you very much.