I'm currently trying to do the integrative analysis of ChIP-seq and RNA-seq data. I used the "ChIPseeker" and "TxDb.Mmusculus.UCSC.mm10.knownGene" package for annotating ChIP-seq peaks. So I understand that the package used the "mm10.knownGene.gtf" file from UCSC (https://hgdownload.soe.ucsc.edu/goldenPath/mm10/bigZips/genes/) for gene annotation (please correct me if I'm wrong). For my RNA-seq analysis, I then used this file in STAR mapping and RSEM quantification, together with the "knownIsoforms.txt" file downloaded from http://hgdownload.cse.ucsc.edu/goldenPath/mm10/database/.
The problem is, a lot of geneID corresponding to peaks obtained from "ChIPseeker" and "TxDb.Mmusculus.UCSC.mm10.knownGene" are not presented in RNA-seq result from RSEM and vice versa. I would like to ask if I used the right file and correct analysis methods or not? If not, what annotation file should be used for my RNA-seq analysis so that I get the compatible result to ChIP-seq peak annotation from "TxDb.Mmusculus.UCSC.mm10.knownGene"?
Best regards, Kasit