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Hi this is more of a question than an issue. I was wondering if NeoLoopFinder can be applied to H3K27ac HiChIP, given the enhancer hijack use case as illustrated in the nature paper? Thanks!
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Hi
I have a more general question about the method here and hope that you can you give me an advise.
I would like to know if this method works well if I input a global HiC dataset (not HiChIP)…
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Hi Caleb,
I am receiving the following error:
```
Traceback (most recent call last):
File "/usr/local/bin/hichipper", line 8, in
sys.exit(main())
File "/usr/local/lib/python2.7/dist…
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Hi !
First of all, thanks a lot for this really nice tool.
I am trying to setup a fresh install of HiC-Pro 3.0.0 on our cluster, but - after successfully running the workflow on the test data se…
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Dear developer,
Thanks for providing this amazing tool for HiC data modeling! After installation, I ran testing on the sample data, however, I got TypeError as follows. I also tried my own data and…
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Hi,
I would like to test including multimappers in my HiChIP datasets which have been analyzed by HiC-Pro and FitHiChIP pipelines before. Can I somehow use .ValidPairs or .allValidPairs from the HiC-…
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Hello Caleb,
We are interested in running hichipper on our HiChIP data. However, your pipelines (Hi-C, capture HiC and HiChIP) are based on HiCUP which results in a bam that contains all the Valid…
rdali updated
6 years ago
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Caleb,
I've gotten hichipper to analyze my HiChIP data if I include a ChIP-seq peak bed file in the .yaml (as opposed to finding peaks in the HiChIP data using MACS2 which was giving me lots of err…
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Hello
I performed hichip and ran HiC-Pro, the results show that my sample have higher trimmed map rate to around 50%. According to the manual :"_abnormal level of chimeric reads can reflect a ligatio…
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Hi! I am using the function plotPairsArches() to plot HiChIP contacts and providing it with values for the arch height. It's not clear to me now to draw an accompanying y-axis that will be in the same…