I was dealing with this package called 'Chipseeker' . I tried annotating a chip-seq peak calls fro Mycobacterium tuberculosis. As there is no 'org.Mtu.eg.db' package for annotation & 'TxDB' can be used in Chipseeker, so I created TxDB package & annotated as follows :
txdb <- makeTxDbFromGFF("./m.tub1.gff3",circ_seqs=character(), organism="Mycobacterium tuberculosis")
peakAnno <- annotatePeak(peak1, tssRegion=c(-3000, 3000), TxDb=txdb, genomicAnnotationPriority = c("Promoter", "5UTR", "3UTR", "Exon", "Intron", "Downstream", "Intergenic"))
Note: GFF was downloaded from ftp://ftp.ensemblgenomes.org/pub/bacteria/release-35/gff3/bacteria_0_collection/mycobacterium_tuberculosis_h37rv/Mycobacterium_tuberculosis_h37rv.ASM19595v2.35.gff3.gz
The chip-seq was done for 'Gyrase' but annotations from Chipseeker gave mostly 'promoters' . Is is correct or am I suppose to add some more steps? Please help me.
Thanking you in advance,