Question: Chip-seq peak annotation [Chipseeker]
1
gravatar for anu014
22 months ago by
anu014160
India
anu014160 wrote:

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

ADD COMMENTlink modified 22 months ago by Guangchuang Yu2.1k • written 22 months ago by anu014160
2

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.

ADD REPLYlink written 22 months ago by Sinji2.8k
2
gravatar for Guangchuang Yu
22 months ago by
Guangchuang Yu2.1k
China/Hong Kong/The University of Hong Kong
Guangchuang Yu2.1k wrote:

For virus/bacteria, tssRegion=c(-3000, 3000) is too large.

ADD COMMENTlink modified 22 months ago • written 22 months ago by Guangchuang Yu2.1k
1

Thank you Guangchuang for the reply :) So how can I optimise the parameter for 'bacteria'? And do parameter 'genomicAnnotationPriority' affects the annotation process in a way that Chipseeker will try to fit promoters first then rest of the types of annotation?

ADD REPLYlink modified 22 months ago • written 22 months ago by anu014160
2

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.

ADD REPLYlink modified 22 months ago • written 22 months ago by Guangchuang Yu2.1k

Can I use the same range for Mouse too? as it's almost similar to human..

ADD REPLYlink written 13 months ago by anu014160
1

yes. mouse is similar to huaman.

ADD REPLYlink written 13 months ago by Guangchuang Yu2.1k

Okay. I'll be using same range for mouse now. Thank you Guangchuang.

ADD REPLYlink written 13 months ago by anu014160
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