Hi all!
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 :
library(GenomicFeatures) 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, Anupriya
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anu014
1 answer
For virus/bacteria, tssRegion=c(-3000, 3000) is too large.
I don't know how to optimise the tssRegion parameter. c(-1000, 1000) or c(-3000, 3000) are commonly used for human. You may need to checkout some references for your species.
Yes, genomicAnnotationPriority parameter will affect the priority of genomic annotation and you can set lower priority of promoter annotation.
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Check your ChIP-seq data on IGV and look at a couple of examples of peak calls. Do they mostly fall in the promoter region? If so, then the annotation is probably correct.