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