Question: ChIP-Seq Analysis allele specific way?
0
gravatar for Susmita Mandal
9 months ago by
Bangalore
Susmita Mandal50 wrote:

Hello everyone,

I am about to do ChIP-Seq analysis allele specific way. I have not done ChiP-Seq analysis practically, but I have some idea about how to do it. The problem is I'm not getting any answers for doing ChIP Seq allele specific way. I have done allele specific RNA Seq analysis. I have the two parental genomes as well. From what I have read so far, after aligning the ChIP-Seq, we do peak calling and it gives us a bed file. So

  1. Is it same as RNA-Seq? Should I align the ChIP reads to both the parental genomes?
  2. After peak calling, should I intersect the bed file to my vcf file like in RNA-Seq or there is another way of doing ChIP-seq allele specfic way?
  3. Or it is not possible altogether and I'm barking the wrong tree?

Any help is appreciated.

Thanks, Susmita

ase macs2 ngs chip-seq vcf • 431 views
ADD COMMENTlink modified 9 months ago by Devon Ryan92k • written 9 months ago by Susmita Mandal50
1
gravatar for Devon Ryan
9 months ago by
Devon Ryan92k
Freiburg, Germany
Devon Ryan92k wrote:
  1. Yes, it's the same. Yes you should align to both (possibly then using SNPsplit).
  2. It's best to call peaks on the merged sample and then quantify according to parent of origin.
  3. It's totally possible.
ADD COMMENTlink written 9 months ago by Devon Ryan92k

Thank you for the response. I have few questions though. How to do SNPsplit? On both the differnet alignment files or should I merge it. and regarding calling peaks, what is the merged sample and how to quantify according to parent of origin?

ADD REPLYlink written 9 months ago by Susmita Mandal50

Read the SNPsplit documentation and everything will be clear.

ADD REPLYlink written 9 months ago by Devon Ryan92k

So far I understood that 1. Align the sample to both the parental genomes. 2. Merge the SAM/BAM file. 3. Use SNPsplit to get tags for allele specific. 4. Run the BAM file for peak calling

Correct me if I'm wrong. And also how to quantify?

ADD REPLYlink written 9 months ago by Susmita Mandal50
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