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Question: Help with Chip-Seq data analysis without input!
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gravatar for iraia.maialen
2.6 years ago by
iraia.maialen • 10
iraia.maialen • 10 wrote:

Hi! I am new in galaxy and I am trying to analyse the sequences of a ChIP-Seq.I have been reading a lot of tutorials for that but I am getting stuck. I have two ChIP-Seq samples, with a Mnase fragmentation, one is the biological control sample (not the input) and the other one is the treated sample. We didn't sequence the input so I can't use it for eliminate the background in the data analysis. So how can I do the peak calling step? I don't think that using the biological control I will get a good result of peaks, and I don't know what is the correct way of doing it. Any help is more than welcome! Thanks
mnase without input chip-seq • 1.7k views
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modified 2.6 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.6 years ago by iraia.maialen • 10
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gravatar for Jennifer Hillman Jackson
2.6 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Both are routinely used in experiments, including those done by the ENCODE consortium. Example article describing the processing (there are many others): http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3431496/

Peaks can also be called with just the single treatment sample. Perhaps run an experiment to see how the results differ: run once with just the treatment, once with the treatment + control, and then compare the two? In the end, this will be a judgement call on your part, but running a few tests will provide more information to base the final protocol decisions on.

Best, Jen, Galaxy team
ADD COMMENT • link written 2.6 years ago by Jennifer Hillman Jackson ♦ 25k
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