HiCCUPS Loops

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Peter Kerpedjiev edited this page Jan 19, 2017 · 2 revisions

HiCCUPS loops list

Example:

chr1    x1      x2      chr2    y1      y2      color   f1      f2      f3      f4      f5
1       144835000       145835000       1       144835000       145835000       255,255,0       0.5517  0.35009 0.2686  0.4308  0.5391

Get the raw data:

wget -P ~/data/raw ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE63nnn/GSE63525/suppl/GSE63525_GM12878_primary%2Breplicate_HiCCUPS_looplist.txt.gz

Whole data

python scripts/tileBed2DFileByImportance.py \
    --assembly b37 \
    --skip-first-line \
    ~/data/raw/GSE63525_GM12878_primary+replicate_HiCCUPS_looplist.txt.gz

aws s3 cp ~/data/raw/GSE63525_GM12878_primary+replicate_HiCCUPS_looplist.txt.gz.multires.db \
       s3://pkerp/public/hg-server/data/

Short data

gzcat ~/data/raw/GSE63525_GM12878_primary+replicate_HiCCUPS_looplist.txt.gz \
    | head -n 1000 > test/sample_data/hiccups_loops_short.txt

python scripts/tileBed2DFileByImportance.py --assembly b37 \
    --skip-first-line test/sample_data/hiccups_loops_short.txt 

cp test/sample_data/hiccups_loops_short.txt.multires.db ~/projects/higlass-server/data/