Question: ChIP-Seq Analysis allele specific way?
0
gravatar for Susmita Mandal
4 weeks ago by
Bangalore
Susmita Mandal20 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 • 165 views
ADD COMMENTlink modified 4 weeks ago by Devon Ryan88k • written 4 weeks ago by Susmita Mandal20
1
gravatar for Devon Ryan
4 weeks ago by
Devon Ryan88k
Freiburg, Germany
Devon Ryan88k 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 4 weeks ago by Devon Ryan88k

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 4 weeks ago by Susmita Mandal20

Read the SNPsplit documentation and everything will be clear.

ADD REPLYlink written 4 weeks ago by Devon Ryan88k

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 29 days ago by Susmita Mandal20
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