Create, manipulate, and visualize cool DNA-DNA interaction files

In [ ]:

    

%%bash
source activate py27
conda install numpy scipy pandas h5py
cooler dump -t pixels --join GSM2644945_Untreated-R1.100000.cool.gz > /output_dir/GSM2644945.txt


    

In [ ]:

    

%%bash
source activate py27
cooler csort hg19.chrom.sizes [input_origami_contact_list]
cooler cload tabix hg19.chrom.sizes:$bin_size  [input_origami_contact_list].sorted.txt.gz  [input_origami_contact_list].cool"
cooler coarsegrain --no-balance  [input_origami_contact_list].cool"


    

In [ ]:

    

!docker exec higlass-container python higlass-server/manage.py ingest_tileset \
    --filename "/data/[input_origami_contact_list].multires.cool" \
    --datatype matrix --filetype cooler --uid cooler-demo


    

In [ ]:

    

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