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Hi!
I would like to know if there is a new tool to generate .fasta, .agp, and .bed files describing the modified assembly file that I obtained from JuiceBox since the tool juicebox_assembly_convert…
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Hi,
I was trying to use jucier_tool version 1.14.08 hiccups to call loops in my hi-c data. The software gave me a warning of sparse data and asked me to enable the --ignore_sparsity flag. But when …
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Another juicebox.js regression. If loading by URL, the "name" of the dataset is "unnamed". It should be the "file" part of the url, that is the bit after the last "/" and before the "?", if any. …
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**Describe the bug**
straw aborts for a `stoi` issue
**To Reproduce**
I have compiled straw on my Mac (tried also with the binary version distributed here) and run it on .hic data provided by a c…
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Hi
I am trying to convert .hic file to mcool. It show error. Here is how it looks.
Header info from hic
... Chromosomes: ['ALL', '1', '10', '11', '12', '13', '14', '15', '16', '17', '18', '19',…
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hi,
Now, I have a ordering and orientation genome final.fasta file. Can we use the validPairs file and final.fasta file to created .hic and .assembly files, which can be loaded by Juicebox Assemb…
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Hello,
I am trying to use HICCUPS utility for loop calling on HiChIP data generated from our lab. We generated .hic file with HiCPro hic2juicebox utility on allValidPairs file. The size of the .hic…
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Hi @gtrichard @joachimwolff ,
I have observed the similar behavior of hicPCA as described in https://github.com/deeptools/HiCExplorer/issues/346
As suggested, I masked the centromere. Most of th…
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Hi,
I have observed that when I plot my iced matrices created using the HIC-Pro pipeline, I usually see areas that seem to lack any interaction across a given region. (Picture below).
![image](http…