Chip-seq peak annotation [Chipseeker]
1
0
Entering edit mode
@anupriyaverma1408-13011
Last seen 5.8 years ago

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

chipseeker chip-seq annotation Guangchuang • 1.4k views
ADD COMMENT
0
Entering edit mode
Guangchuang Yu ★ 1.2k
@guangchuang-yu-5419
Last seen 6 months ago
China/Guangzhou/Southern Medical Univer…

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

ADD COMMENT

Login before adding your answer.

Traffic: 716 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6