Question: chip-seq analysis and peak annotation
0
gravatar for tarek.mohamed
23 months ago by
tarek.mohamed250
tarek.mohamed250 wrote:

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

chip-seq • 1.5k views
ADD COMMENTlink modified 23 months ago by Sinji2.8k • written 23 months ago by tarek.mohamed250
1
gravatar for EagleEye
23 months ago by
EagleEye6.3k
Sweden
EagleEye6.3k wrote:

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.

ADD COMMENTlink modified 23 months ago • written 23 months ago by EagleEye6.3k
0
gravatar for Sinji
23 months ago by
Sinji2.8k
UT Southwestern Medical Center
Sinji2.8k wrote:

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.

ADD COMMENTlink modified 23 months ago • written 23 months ago by Sinji2.8k
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