The data I use is ENCFF424GON. When I use ENCODE ChIP-seq pipeline on DNAnexus and use SPP(xcorr) to calculate the estimated fragment length, it gives me 140bp, however, when I use macs2 predictd function with parameter -g hs -m 5 50, it gives me 274bp. I try several mfold combinations but no one close to 140bp. I just wondering why there is so much difference between these two algorithms. It seems both of them use cross-correlation method to decide the estimated fragment length but the results are not even closed.
Thanks in advance! Kun