Question: MACS for ChIP seq of histone modifications in S. cerevisiae
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gravatar for Law, Michael J.
3.8 years ago by
United States
Law, Michael J.20 wrote:

I am performing ChIP-seq of histone modifications in S. cerevisiae. The trouble occurs when I am using MACS. If I use the correct genome size of 1.2e+7 and almost any value of MFOLD (as low as 3), I don't get any peaks. If the only parameter I change is the genome size to 2.7e+9, I get peaks, albeit they are not correct.

Since it is histone mods and not TF binding, is MACS even appropriate to use? Would SICER be a better choice?

macs chip-seq • 1.1k views
ADD COMMENTlink modified 3.7 years ago by Jennifer Hillman Jackson24k • written 3.8 years ago by Law, Michael J.20
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gravatar for Jennifer Hillman Jackson
3.7 years ago by
United States
Jennifer Hillman Jackson24k wrote:

Hello,

You may have tested this out by now, or reviewed the documentation, but SICER would be a good choice. 
http://home.gwu.edu/~wpeng/Software.htm

Take care, Jen, Galaxy team

ADD COMMENTlink written 3.7 years ago by Jennifer Hillman Jackson24k
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