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Peter Kerpedjiev edited this page Jan 18, 2017 · 20 revisions

BigWig files

python scripts/tile_bigWig.py \
   ~/Downloads/wgEncodeCaltechRnaSeqHuvecR1x75dTh1014IlnaPlusSignalRep2.bigWig \
   --output-file  \
   ~/Downloads/wgEncodeCaltechRnaSeqHuvecR1x75dTh1014IlnaPlusSignalRep2.hitile

Arrowhead domains list

Example:

chr1    x1      x2      chr2    y1      y2      color   o       e_bl    e_donut e_h     e_v     fdr_bl  fdr_donut       fdr_h   fdr_v   num_collapsed   centroid1       centroid2       radius
10      100225000       100230000       10      100420000       100425000       0,255,255       95      27.4926 25.533  31.2977 32.8853 1.19563917441e-15       9.93567880311e-16       3.82998212108e-10       4.0995892129e-10        10      100228000       100426000       10606.6017178

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

Aggregate it into tiles:

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

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

Create a shorter test set:

gzcat ~/data/raw/GSE63525_GM12878_primary+replicate_Arrowhead_domainlist.txt.gz | head -n 1000 > test/sample_data/arrowhead_domains_short.txt

python scripts/tileBed2DFileByImportance.py --assembly b37 --skip-first-line test/sample_data/arrowhead_domains_short.txt
cp test/sample_data/arrowhead_domains_short.txt.multires.db ~/projects/higlass-server/data/

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

Aggregate to tiles:

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_Arrowhead_domainlist.txt.gz.multires.db \
       s3://pkerp/public/hg-server/data/
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