Question: Chip-seq peak annotation [Chipseeker]
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gravatar for anupriyaverma1408
2.4 years ago by
anupriyaverma14080 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 2.3 years ago by Guangchuang Yu1.1k • written 2.4 years ago by anupriyaverma14080
Answer: Chip-seq peak annotation [Chipseeker]
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gravatar for Guangchuang Yu
2.3 years ago by
Guangchuang Yu1.1k
China/Guangzhou/Southern Medical University
Guangchuang Yu1.1k wrote:

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

ADD COMMENTlink written 2.3 years ago by Guangchuang Yu1.1k
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