File formats

gcMapExplorer uses three format of files. Both gcmap and genomic track file are in HDF5 format while ccmap file is in numpy memmap format.

• gcmap file
  • Structure of gcmap file
  • Compression
  • Portability and Readability
  • Convert Hi-C data to gcmap
    • coo2cmap : convert COO sparse matrix format
    • pairCoo2cmap : convert pair COO sparse matrix format
    • homer2cmap : convert HOMER Hi-C matrix format
    • bc2cmap : convert Bin-Contact pair files
    • hic2gcmap : convert hic files
    • cmapImporter : An application to convert Hi-C formats to ccmap/gcmap
• ccmap file
  • Why two files?
  • Advantages of memory mapped matrix file
  • Contents of *.ccmap file
• genomic track HDF5 (h5) file
  • Downsampling or Coarsening of datasets
  • Structure of genomic track (.h5) file
  • Compression
  • Convert bigWig/wig/bed to genomic track h5 file
    • h5Converter : A GUI application to convert bigWig/wig/bed
    • bigwig2h5 : convert bigWig to h5
    • wig2h5 : convert wig to h5
    • bed2h5 : convert bed to h5
    • encode2H5 : download and convert ENCODE datasets to h5