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Old 01-14-2016, 12:37 PM   #3
Senior Member
Location: MA

Join Date: Oct 2010
Posts: 160

Hi all,
And what about MeDIP-seq (not ChIP-seq)? I guess the answer would be the same, but what parameters keep/change?
I'm working on a Illumina IP library (50 bp SE) made after inmunoprecipitate genomic DNA fragments with antibodies which detect methylated bases. I've seen one paper using MACS with these kind of data, thought no specify any parameters used. Right now, I don't have control/input.
Eg. after using MACS, it says no paired peaks were found so I should go with the --nomodel option, but I'm guessing about --shiftsize since there is no TF I'm looking for (just nucleotide methylation); would it be important that --shiftsize number?
One more thing I'd like to ask is, not having control/input I've heard I should use the --nolambda option. Actually that's from this ppt tutorial:

Any thought/inputs would be appreciated. Thanks

Last edited by cascoamarillo; 01-14-2016 at 01:38 PM.
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