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Possibly related to https://github.com/XiaoTaoWang/NeoLoopFinder/issues/6#issuecomment-884874868 . I successfully called neoloops in my sample using neoloop-caller. Adapting code from this repo's read…
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I'm working on a relatively big genome (~20Gbp), and I want to create an assembly hic-file that can be used for editing in Juicebox. Previously I have created hic-files for individual chromosomes usin…
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Hi!
We've updated straw quite a bit, and specifically, there are new updates in version 9 of the .hic file format that requires using the latest version of straw. In order for users to use this too…
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Extra lines dumped when dumping norm vector
When I run juicebox dump norm KR .. by using 50kb as the bin size, the correction vector it returned always contain more lines that it should be. For examp…
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For the long-term sustainability of the code, we should make all variables have meaningful names; e.g. targetVector or indicesToIgnore rather than z, b, etc. Ideally we also make them match the names …
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Hi, I got an error about "NameError: name 'pp' is not defined".
My command: "centromics -p 128 -l $hifi -g V127_CBMhap1.fasta -pre V127_CBMhap1-hifi_hifi -hic ./juicer/aligned/merged_nodups.txt"
…
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Hi, I am using straw with the following command:
`./straw NONE myfile.hic Y:1:15902555 Y:1:15902555 BP 100000 > outfile`
I get following error:
"File doesn't have the given chr_chr map."
However…
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Hello, I would like to use hifi and hic data to find the centromere sequence of the genome.
However, when using HIC data, a Juice Box interface may appear. Then I imported merged_nodups.hic file, and…
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[saved_saves.xml.txt](https://github.com/theaidenlab/Juicebox/files/67506/saved_saves.xml.txt)
INFO [2015-12-19 09:47:38,506] [GenomeManager.java:174] [pool-1-thread-1] Genome loaded. id= hg19
jav…
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For bedgraph files:
Bedgraph files when loaded give the following error:
**Could not load resource: IGV has not been initialized error on loading a bedgraph file.**
When gzipped, this error goes away…