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I would like to use the command line functionality of hicexplorer to automatically plot hic matrices as part of my workflow. I have generated `.hic` files that can be loaded by Juicebox for manual ed…
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### Ask away!
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I was able to successfully use the pipeliine to output in `out/juicebox_input/out_JBAT.assembly` and `out_JBAT.hic` files and then subsequently make the required changes in Juicebox.
Following the …
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Hi, I'm having trouble downloading Hi-C data for chromosome 9 specifically using juicebox. When I use juicebox, it creates 2 files (chr9.KRobserved.gz. and chr9.KRNorm.gz) respectively, but both files…
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Hi,
I downloaded the new version of the pipeline and reinstalled it from the start to make sure everything was updated. I tried running the test command you provide in the readme:
`snakemake --use…
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Hello,
Great program (if I could get it to work)! I am trying to run predict.py after running hic steps for juicebox data (juicebox_dump.py, compute_powerlaw_fit_from_hic.py). The steps to get nei…
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Thank you for publishing this! I've "dockerized" this with the following Dockerfile
```
FROM python:latest
RUN git clone https://github.com/snicker/juicepassproxy
RUN pip install -r juicepassp…
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When running the snakemake workflow, on K562 Chr22 example, I get this error
`python: can't open file '/home/oweyi/week_2/issue/encode_e2g_features/workflow/scripts/compute_powerlaw_fit_from_hic.py':…
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Hello xiaofei,
My commands are as follows
```
Haphic=/data/Erick_Tong/software/HapHiC-main
ln -s ../01hifiasm_hfhc/XH01_asm.hic.p_utg.fa asm.fa
ln -s ../01hifiasm_hfhc/00data/XH01_all_hic_R1.fq.g…