According to ENCODE recommendations
For broad-peak histone experiments, each replicate should have 45 million usable fragments
According to my understanding, a usable fragment means a uniquely mapped read / pair of reads.
H3K9me3 is an exception as it is enriched in repetitive regions of the genome. ... Tissues and primary cells should have 45 million total mapped reads per replicate.
I fail to grasp Encode's language.
- Does "total mapped reads" mean uniquely mapped reads?
- If so, why is 45 million "an exception" ? It is the same as the other broad peaks.
Any ideas where else can I look for an explanation?