Correlation analysis of HiTag and in situ Hi-C.
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- Starting from loop to compare, reference,but notice the factor is Cohesin(Smc1a )
- On the other hand, The original article says:
"...The same parameters used for GM12878 Hi-C were used on the HiChIP data sets as follows: hiccups -m 500 -r 5000,10000 -f 0.1,0.1 -p 4,2 -i 7,5 -d 20000,20000 HiCCUPS_output.txt."
As above, we should know that it is not a good choice to do correlation analysis of HiTag and in situ Hi-C by a direct way.
There is another choice Read-normalized in situ Hi-C and HiChIP raw maps
Ours
Fellow HiCAR
(B) Normalized signal in a window of 3kb on each side of ATAC-seq peaks for HiCAR R2 (red), HiCAR R1 (blue) and in situ HiC (black).
(C) Normalized signal in a window of 2kb around TSS for HiCAR R2 (Red), Trac-looping (green), Ocean-C (orange), in situ HiC (blue).
About the cells and unique-PETs, we can note in the example of heatmap
(D) Comparison of input cells number and sequence outputs across different methods.
compare the distance of loop
(E) Percentage of unique short range cis, long range cis and trans reads ratio for HiCAR, in situ HiC and Trac-looping.
(F) contact frequency as a function of distance measured by HiCAR, in suit HiC and Trac-looping.
(G) Heatmap of aggregated contact matrix at a resolution of 10kb around indicated histone marker peakset. (top panel, HiCAR; bottom panel, in situ HiC).
ours
(K-L). Scatter plots show the reads counts from HiCAR RNA profile and bulk polyA RNA-seq dataset and HiCAR ATAC-profile and bulk ATAC-seq dataset.
(M) Venn diagram showing the overlap of HiCAR ATAC peaks and bulk ATAC-seq peaks from 4DN data portal.
(N) Boxplots show the MACS2 confidence scores of ATAC-seq peaks that overlap and do not overlap with each other.
call 1D-peak : use all reads
call 1D-peak : use self... reads
如果HiTag的有效数据量与CUT&Tag的有效数据量一致的情况下，他们所得的peak是否存在差异。