HPV genes visualization on IGV

Question

[amir.saeidian]

I have detected various HPVs from RNA-Seq data. I need to see the particular detected HPV on IGV to see if it is real and not noise and to see particular HPV genes like L1. I can not visualize the unmapped_aln_sorted.bam file on IGV as I can not find the HPV genome in IGV? Any suggestion? Any alternative solution? Thank you!

[GenoMax]

It is easy to build a custom genome in IGV for such an application.

Answer 1

[desouzareis.r]

You can find a list of different HPV genomes at https://www.ncbi.nlm.nih.gov/assembly/organism/337041/latest/ and then access and download the FASTA and GFF files for the chosen HPV genome. After, you can load both files to the IGV application