Hi all, In this paper (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9831945/) the authors use a reference genome that includes the HIV genome. Seen in this sentence of the paper:
"Adapters and low-quality bases were trimmed using Cutadapt v1.18 software 11 before alignment with the human reference genome(hg38andHIV-1: NC_001802.1) and GENCODE annotation v30 using STAR 2.7.0f. 12"
Searching for NC_001802.1 directs to a page (https://www.genome.jp/dbget-bin/www_bget?refseq:NC_001802) that contains the complete HIV genome which is expected.
Thus my question is how might I go about integrating the HIV genome into my human reference genome. The paper linked above uses STAR but I prefer to use HISAT2 as it can easily run on a laptop. To do this using HISAT2 I believe I would have to combine the two genomes into one before building my indices. Any suggestions are appreciated.