Data Statistics
Input Samples
Distribution of the rRNA and whole genome mapping ratios of reads from input samples of m6A-seq and MeRIP-seq data.
IP Samples
Distribution of the rRNA and whole genome mapping ratios of reads from IP samples of m6A-seq and MeRIP-seq data.
PCR Duplicate Proportion (PDP)
Distribution of PDP in input and IP samples of m6A-seq and MeRIP-seq data. PCR duplicates were evaluated by MarkDuplicates from Picard.
\[ PDP = {\text {# of PCR duplicate reads} \over \text {Total number of mapped reads}} \]
Non-Redundant Fraction (NRF)
Distribution of NRF in input and IP samples of m6A-seq and MeRIP-seq data. NRF was measured according to the ENCODE standards.
\[ NRF = {\text {# of distinct read-mapped genomic locations} \over \text {Total number of read-mapped genomic locations}} \]
PCR Bottlenecking Coefficient 1 (PBC1)
Distribution of PBC1 in input and IP samples of m6A-seq and MeRIP-seq data. PBC1 was measured according to the ENCODE standards.
\[ PBC1 = {\text {# of one-read-mapped genomic locations} \over \text {# of distinct read-mapped genomic locations}} \]
PCR Bottlenecking Coefficient 2 (PBC2)
Distribution of PBC2 in input and IP samples of m6A-seq and MeRIP-seq data. PBC2 was measured according to the ENCODE standards.
\[ PBC2 = {\text {# of one-read-mapped genomic locations} \over \text {# of two-reads-mapped genomic locations}} \]
exomePeak vs MACS2
Distribution of Jaccard index (JI) and Simpson index (SI) for the comparisons of peaksets from exomePeak and MACS2.
exomePeak vs MeTPeak
Distribution of Jaccard index (JI) and Simpson index (SI) for the comparisons of peaksets from exomePeak and MeTPeak.
MeTPeak vs MACS2
Distribution of Jaccard index (JI) and Simpson index (SI) for the comparisons of peaksets from MeTPeak and MACS2.
Definition of JI and SI
\[ JI = {{A \cap B} \over {A \cup B}}, SI = {{A \cap B} \over min(A, B)} \]
A: Peakset A
B: Peakset B
Histone ChIP-seq Samples
Distribution of sample and dataset counts of histone ChIP-seq data from ENCODE.
DNase-seq Samples
Distribution of sample and dataset counts of DNase-seq data from ENCODE.
Histone Marks
Distribution of sample counts of distinct histone marks.