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Hi,
I'm trying to run `Juicer` in order to use `3d-dna`. Everything seems to work fine with the data you provide, but when I execute it on my data I get a number or warning messages and some errors…
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I am running on chr10_intrachr Hi-C data of rao.(GM12878) by " -m 3" usage
there are 128M cis PETs in this chr
and I find that over 50Gb memory is used and cloops keeps running after 1 day.
So, w…
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I get the following error after isntallation and running the test script:
[seb@pc examples]$ sh run.sh
2019-05-03 18:39:59,823 INFO Command line: cLoops -f GSM1872886_GM12878_CTCF_ChIA-PET_chr21_h…
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Phase refers to the following...
>Juicebox correction resulted in a final set of 18 scaffolds spanning 942 Mbp, with these scaffolds having a scaffold N50 of 57,743,597 Mbp and a scaffold N90 of 34,9…
sr320 updated
5 years ago
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Hi :
Seems like the output of `Eigenvector` is oriented randomly for each chromosome , Is there a parameter to flip the values to have a positive correlation with some tracks associated with act…
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Hi,
I want to analyze some files for which I dont have the raw data, only hic files. I wonder if it is possible to use cLoops with hic file by extracting the data as a sparse format using a'juicer_t…
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Hi, I am using cLoops to call loops on my HiC datasets (>200M valid pairs/sample), and I am trying to tune the parameters to incrase and or decrease the number of called loops. Could you explain how t…
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Hi Jim,
Nice to see juicebox.js can access GEO hic files through web.
I also tried [this link](https://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2583nnn/GSM2583729/suppl/GSM2583729_H3K27ac_HiChIP_2.hic)…
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Hi,
I'm playing with straw.cpp and the file https://github.com/aidenlab/Juicebox/blob/master/data/inter.hic that I saved on my side as 'jeter.hic'
```
$ wget -q -O - "https://github.com/aidenlab/…
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Hi, is there a way of finding all the interacting points of any single locus using Juicebox?