BSgenomes for HIV viruses

Question

[xiaoleiusc]

Dear Biostars users,

I wonder if there are BSgenomes available for HIV viruses? I am trying to identify clusters from CLIP-seq data mapping to the HIV genome with wavClusteR. I stuck at one step as below:

`require(BSgenome.Hsapiens.UCSC.hg19)

wavclusters <- filterClusters( clusters = clusters, highConfSub = highConfSub, coverage = coverage, model = model, genome = Hsapiens, refBase = "T", minWidth = 12)

wavclusters`

I basically want to replace the BSgenome.Hsapiens.UCSC.hg19 with HIV genomes. If there are no available BSgenomes, I guess I have to ask how to create a custom genome in this case. Any input is appreciated.

Thanks ahead,

Xiao

Answer 1

[ATpoint]

Forging custom BSgenomes is outlined in detail here: https://www.bioconductor.org/packages/devel/bioc/vignettes/BSgenome/inst/doc/BSgenomeForge.pdf

You can check at the bottom of the page which genomes already exist, https://bioconductor.org/packages/release/bioc/html/BSgenome.html, see the Depends On Me slot.