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Old 05-29-2012, 08:53 AM   #1
dpryan
Devon Ryan
 
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Default MeDIP-seq peak calling (with replicates)

Hi all, I'm curious what people are using these days for finding peaks in MeDIP-seq data (I have two experimental conditions, each with replicates, and I'm interested in finding changes between them). I've browsed through a number of common tools, such as MACs, but they seem to suggest pooling biological replicates into a single .bed file for further analysis. I would assume that it's beneficial to exploit the presence of replicates for judging noise and am wondering if there's something else out there. Alternatively, if someone can point me to where this sort of issue is discussed in the MACs manual I'd appreciate it.

Alternatively, do people recommend using MACs or a similar tool to give a first pass at finding peaks, which can then be used as regions of interest for other tools (which I suppose I could just write, but I assume others have already done that).
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Old 05-30-2012, 01:27 AM   #2
simonandrews
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We wouldn't normally do peak detection for MeDIP as you'll end up selecting for high CpG content regions. We prefer to systematically analyse all regions (often splitting up by type - exons, promoters etc) which will still have some bias because of differing levels of observations, but does allow you to spot interesting things.
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Old 05-30-2012, 02:58 AM   #3
rory
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We have analyzed MeDIP both using peak callers (MACS) and pre-defined regions (promoters, 3'UTR, introns, etc.). In any case, we keep the replicates separate, deriving different peaksets for each replicate in the peak-calling case.

One we have peaks, we use the Bioconductor package DiffBind, which allows you to derive a consensus peakset, and then uses the distributions of enrichment scores in the replicates to identify differentially methylated regions.
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Old 05-30-2012, 04:00 AM   #4
dpryan
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rory: Thanks that makes sense and was what I figured needed to happen. I expect I'll just create a couple .bed files and merge them with bedtools prior to the normal count based tools used for everything else.

simon: Unfortunately in my case we expect to not see any systemic regional (i.e., exons, promoters, etc.) differences between the datasets. I'll run those analyses anyway since that should be done anyway though.

Thanks all
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Old 10-20-2014, 08:45 AM   #5
drdna
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I would like to use diffbind for differential peak calling on peaksets generated using macs2. However, I cannot find information on the required format for the input peakset. Research tells me that the fourth column contains a "confidence' value. My guess is that this should be either the P-value or Q-value in the peaks.xls files coming from macs2. Please can someone enlighten me? Thanks.
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Old 10-20-2014, 09:09 AM   #6
rory
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The easiest way to read MACS peaks into DiffBind is to specify the .xls files in the sample sheet and specify "macs" as the peak caller (either in a column of the sample sheet, or using the peakCaller="macs" in the call to dba(). This will use p-value as the score. Alternatively, you can convert the .xls to tab-separated text files, with the first three columns being the chromosome, start, and end of each peak, followed by as many score columns as you want. then set scoreCol= whichever column you want to use as a score.

Ultimately, which peak caller scores shouldn't matter much, as they will be discarded after you call dba.count() to determine the enrichment for each merged peak in every sample.

Cheers-
Rory
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