chip-seq analysis and peak annotation

Question

[tarek.mohamed]

Hi All, I am analyzing chip-seq data. I did the alignment using bowtie using hg38 as a reference genome, and peaks calling using macs2. Now I am using R package "chipseeker" to annotate these peaks which needs a txdb object.

My question is can I use txdb of hg19 to annotate peaks, however I used hg38 genome as reference during alignment.

Thanks, Tarek

Answer 1

[EagleEye]

Try homer annotate peak to annotate your peaks with hg38 annotation (GTF). Remember you should always maintain the same genome/gene/transcript annotation throughout your analysis.

Answer 2

[Sinji]

As another option, you can use ChIPseeker to annotate to the hg38 genome in the exact same way you are probably using hg19 (I assume you are following the Bioconductor guide). All you need to do is download and install this reference package and use it as your txdb object.

If you did not use a UCSC reference genome, then use a GTF file to generate your own txdb annotation using the GenomicFeatures R package.