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Hi,
I am using hichipper and diffloop to analyse my H3K27Ac HiChip data. Is that a way to convert hichipper output into .hic file for JuiceBox visualization?
Thanks,
Ana
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Hi,
I'm trying to use MAPS for my HiChIP data, and I have HiCPro output. I'm wondering dose it possible to use HiCPro output for MAPS? which is compatible with many other tools.
Thanks,
Jphe
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Hi,
Caleb and Martin.
I have an issue with diffloop. I have 16 HiChIP samples, 1 control and 4 cancer cell lines, processed by HiC-Pro and hichipper to fetch loops. No I am interested in finding lo…
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Hello,
Thanks for the great tool, I have run into the following error which means Fithichip is not able to compute the statistical significance of input interactions. I am running Fithichip throug…
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Hi Henry, thanks for the help. I could change the grid and background colour now. I have a new problem. I am trying to plot HiChIP, ATAC, ChIP, RNA seq data. Within each track plotted I have a gap, is…
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I am using hichipper to analyze the hichip data of GM12878 which is provided in the qc reports,but I have some questions about the result.I got a different result than the qc report except the Total_P…
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Hello,
I have a question regarding figure 2 in your paper. The figure said the recalls are 60%~80% when using ChIA-PET or HiChIP data as target. But peakachu's prediction is around 15K, and the num…
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Hi, First thank you for providing excellent documentation on FitHiChIP!
I am running FitHiChIP on my HiChIP data generated from HiCPro (.allValidPairs). I am using the following parameters.
```
I…
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Hello,
I got the following error, and I cannot find .mango file in the output folder. Could you help me with this? Thank you!
$ hichipper --out raw-1h-rep1_out_hichipper --macs2-genome mm -mu co…
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FitHiChIP is an explicit and clearly written normalization method for HiChIP data processing.
Beyond significant loop calling, I want to develop a genome-wide background model by using FitHiChIP-prod…