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Can not make the juice dump HiC data for chr9 on K562_combined_30.hic with resolution lower than 25000 #238

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nttg8100 opened this issue Sep 14, 2024 · 0 comments

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@nttg8100
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The HiC data published by NG2019 seems miss the resolution at chr9.
I check on the latest version with this
https://github.com/broadinstitute/ABC-Enhancer-Gene-Prediction/blob/main/workflow/scripts/juicebox_dump.py
or the old version with with branch NG2019
#Download hic matrix file from juicebox

python src/juicebox_dump.py \
--hic_file https://hicfiles.s3.amazonaws.com/hiseq/k562/in-situ/combined.hic \
--juicebox "java -jar juicer_tools.jar" \
--outdir example/input_data/HiC/raw/ \
--chromosomes 9

I manually check and found this command cause the error

java -jar /opt/juicer_tools.jar dump norm KR K562_combined.hic 9 BP 5000 hic/chr9/chr9.KRnorm

then I replace with 10k,15k, and the 25k is the smallest resolution that I can run with this.

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