Descrepancy with MACS model parameter for ChIP-Seq in tumor samples for Histone modifications
Entering edit mode
8.2 years ago
ivivek_ngs ★ 5.2k

Dear All,

I would like to ask a question regarding the usage of MACS default parameters for histone modifications for ChIP-Seq data am interrogating. I am running both MACS1.4 and MACS2 on a large cohort of samples , basically for different histone marks like K27me3,K4me1,K4me3 and K27ac. In my case I have treatment and control but still I tried to use the MACS model to see what is the predicted fragment length and the number of peaks obtained by MACS(both by 1.4 and 2). Usually I have seen that people use --nomodel parameter to bypass MACS modelling but from the Feng et al, 2012 paper (Nature Protocols ,2012) what I understood is if the MACS predicted fragment length is less then it is better to go for --nomodel parameter as written in the paper. Since it correlates to much less coverage. In my samples most of the time MACS predicted fragment length have been between 200-350 bp and creating high number of peaks. Strangely for 4 samples the predicted fragment length have been between 51-53 bp however it gave high number of peaks but for one the number of peaks is quite low. Below is the metrics. I am thinking on now running MACS on all these 4 samples (both 1.4 and 2) using --nomodel parameter, even if for some I have high number of peaks. Since the predicted fragment length is too low. What is the understanding of using --nomodel. I could not find anything more than this of using --nomodel parameter. If someone has some better understanding kindly elucidate or if am I thinking it the wrong way. I would like to have some suggestions from experts who have more experience since I have recently started with ChIP-Seq analysis.

Samples                              MACS1.4_predicted_FL  MACS2_predicted_FL  MACS1.4_peaks  MACS2_peaks
Ascites_K4me1_macs14_out_peaks.bed   52                    52                  158975         61835
Ascites2_K4me1_macs14_out_peaks.bed  51                    51                  86460          21317
Tumor1_K27me3_macs14_out_peaks.bed   53                    53                  72299          45054
Tumor1_K4me1_macs14_out_peaks.bed    52                    52                  457            38
ChIP-Seq macs2 macs1.4 tumor • 2.5k views
Entering edit mode

Do you have any idea of the fragment size from the Bioanalyzer traces? Do you have input data for each sample?

My suspicion is that sample "Tumor1_K4me1_macs14_out_peaks.bed" ChIP has not worked very well and the profile is flat like input. You could check whether it is flat or peaky by comparing your data to ENCODE ChIP-seq and input for the same mods with UCSC browser (try chr22 in wig format) or in IGV.


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