Viewing chimeric reads on IGV

Question

[heir_of_isildur88]

Hi all,

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.

[Medhat]

I think you could use savant It may help in better visualization

It will give you some arch picture that you can easily follow

Answer 1

[Joseph Hughes]

Using the Sashimi plot option in IGV is a good solution. You need to import a bam/sam file that contains chimeric reads. Using HISAT2 to align the reads did enable me to see chimeric reads.

[d-cameron]

Does that work for chimeric reads that use the SA SAM tag, or just for RNA-Seq CIGAR "N" alignments?

[Joseph Hughes]

Not sure about the SA tag but definitely works with the N cigar value.