GIVE interaction format data conversion from different Hi-C contact matrices

To be compatible with different Hi-C contact matrices data types, users can follow these procedures to convert certain Hi-C data to the BED format required by GIVE.

1. hic format from juicer (e.g. hic2bed strawDir hicFile outputFile binSize):
   • Download straw and make sure it is executable.
   • Download script tool in GIVE-Toolbox hic2give.sh and make sure it is executable.
   • Run hic2give.sh as:

     bash ./hic2give ./ test.hic giveInteraction.bed 40000
     

   • Four parameters are required for the command (please input the parameters with the following order):
     • straw file directory,
     • hic file (file extension must be .hic),
     • output file name (with directory if user wish to save the file desired path),
     • bin size that user wants to extract the data from (please make sure the bin size you entered is contained in the hic file).
   • An optional parameter can be provided in the fifth parameter position to indicate the name type of chromosome. The default chromosome names are “chr1”, “chr2”, “chrX” and so on. If you set it as “nochr”, it means chromosome names in the .hic data are “1”, “2”, “X” and so on.
2. Contact matrices derived from GITAR
   • Download gitar2give and make sure it is executable.
   • Run gitar2give. Two parameters are required for the command (please input the parameter with the following order):
     • directory to HiCtool generated normalized_enrich files,
     • output file name prefix.
3. Other contact matrices or genomic interaction data formats
   • As there isn’t a golden standard format of contact matrices and genomic interaction, many other kinds of formats are used in different data sets. Users need to write a script to convert any other data format to GIVE interaction data format.
   • Tutorial 4.1 and tutorial 4.2 are two good examples of converting other genomic interaction format to GIVE format.