How can I use Rat genome for CHIPseeker?

Question

[liusongyan]

I am analyzing my Chip-seq data with CHIPseeker. I really like to features. However, I want to know how I can use this application with different genomes, like Rat or mouse?

Many thanks,

Answer 1

[Guangchuang Yu]

please tag your post with chipseeker, so that I can receive email notification.

Please read the vignette, https://www.bioconductor.org/packages/release/bioc/vignettes/ChIPseeker/inst/doc/ChIPseeker.html#peak-annotation :

TxDb object contained transcript-related features of a particular genome. Bioconductor provides several package that containing TxDb object of model organisms with multiple commonly used genome version, for instance TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene for human genome hg38 and hg19, TxDb.Mmusculus.UCSC.mm10.knownGene and TxDb.Mmusculus.UCSC.mm9.knownGene for mouse genome mm10 and mm9, etc. User can also prepare their own TxDb object by retrieving information from UCSC Genome Bioinformatics and BioMart data resources by R function makeTxDbFromBiomart and makeTxDbFromUCSC. TxDb object should be passed for peak annotation.