Correlation analysis of HiTag and in situ Hi-C.

[wbszhu]

1. Starting from loop to compare, reference,but notice the factor is Cohesin(Smc1a )
2. 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.

[wbszhu]

There is another choice Read-normalized in situ Hi-C and HiChIP raw maps

Ours

[wbszhu]

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).

[wbszhu]

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.

[wbszhu]

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.

[wbszhu]

(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

[wbszhu]

(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.

[wbszhu]

(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

[wbszhu]

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。

[wbszhu]

hicar