I used Bowtie2 to align the reads to the wheat reference,first,I used the first version as the reference, the first version is assemblied as scaffold,the genome side is about 4.6G,I compared the peak between the duplicates and found 65% has overlap, then I think the reproducibility of the two experiments is better.then I used the new assembly chromosome levels reference (14.6G),and has only 33% overlap peaks in the same data sets,so I am confused, I don't know what is the problem? Is my experiments is not good so the repeatability is so poor? or my analysis of the data has some unthoughtful? or due to the genome repeats and transponsons are so many?
Thanks for your insights.