Question: Possible reason for no peaks generated by MACS2
gravatar for Louis Kok
13 days ago by
Louis Kok10
Louis Kok10 wrote:

Hi, I am new to ChIP-Seq data analysis. In my samples, the expression of transcription factor of interest was observed to be down-regulated. Subsequently, a ChIP-Seq on this transcription factor of interest in three replicates was performed and input DNA was used as control. Initially when I performed MACS2 analysis using the command below:

mac2 callpeak -t treatment.rep1.bam treatment.rep2.bam treatmen.rep3.bam -c input.rep1.bam input.rep2.bam input.rep3.bam -f BAM -g hs -n output.macs2

The run failed and I received the error below:

WARNING @ Wed, 10 Oct 2018 11:53:34: Too few paired peaks (0) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead.

After adding --nomodel to the command. The run was successful but not peak was outputted.

My question is: Is it expected for no peak to be detected for samples with down-regulated TF? Or should I further optimize the parameters to increase the chance to get some peaks?

I was wondering if there might be at least some peaks detected due to noise.

Thanks in advance.

chip-seq macs • 107 views
ADD COMMENTlink written 13 days ago by Louis Kok10

If you heavily knock-down TF expression it's unsurprising that there are no peaks. I wonder, how well the library prep worked. Were you able to get decent amounts of DNA from the IP still? Have you looked at a fingerprint from plotFingerprint? If you got a decent amount of DNA still and the fingerprint looks OK then often playing around with --slocal and --llocal helps.

ADD REPLYlink written 13 days ago by Devon Ryan85k
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