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broadinstitute / ABC-Enhancer-Gene-Prediction

Cell type specific enhancer-gene predictions using ABC model (Fulco, Nasser et al, Nature Genetics 2019)
MIT License
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chr9 Hi-C data #188

Closed TakuroIwami closed 8 months ago

TakuroIwami commented 8 months ago

Hi, Thank you for providing us such a nice function. I tried to download Hi-C data following your guidance, described in "Pipeline to Download Hi-C data" Code I used is below,

Download hic matrix file from juicebox

python src/juicebox_dump.py \ --hic_file https://hicfiles.s3.amazonaws.com/hiseq/k562/in-situ/combined_30.hic \ --juicebox "java -jar juicer_tools.jar" \ --outdir example_chr22/input_data/HiC/raw/

Though all the output files were created, only chr9 file was empty. I would appreciate it if you could confirm this matter.

Best regards, Takuro

atancoder commented 8 months ago

I would recommend utilizing the new version of the pipeline: https://github.com/broadinstitute/ABC-Enhancer-Gene-Prediction/tree/main