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Welcome to the ExonUnion wiki!

To create a graph, two input files are needed.

1. exon union file, which contains a union of transcripts of each gene. Formatted in the following way:

   1 ['1034'] ['NM_130786'] chr8 ['-'] [58858171] [58864865] [58858387] [58864803] 8[[58858171, 58858395], [58861735, 58862017], [58864293, 58864563], [58862756, 58863053], [58863648, 58863921], [58864657, 58864693], [58858718, 58859006], [58864769, 58864865]][0] ['A1BG'] ['cmpl'] ['cmpl'] ['1,1,1,1,1,1,1,0,\n']

   • The first column has the gene's unique id
   • The 3rd column is an array of transcripts
   • the 6th and 7th column are arrays of starts and ends of each transcript respectively
   • The 11th column contains an array of array of start and end of each exon.

2. Individual transcripts file

1 1034 NM_130786 chr19 - 58858171 58864865 58858387 58864803 8 58858171,58858718,58861735,58862756,58863648,58864293,58864657,58864769, 58858395,58859006,58862017,58863053,58863921,58864563,58864693,58864865, 0 A1BG cmpl cmpl 1,1,1,1,1,1,1,0,

• first column has the gene unique id/name
• third column is the name of the transcript
• 6th and 7th columns are the start and end of the transcript
• 11th and 12th columns are the starts and ends of exons

These two files must be sorted in the same way, thus the order of the gene unique ids must be the same in both files.

After obtaining these two files, then the json file needs to be created that contains the data for the D3 graph. This is done by running the following command:

  `python script.py [name of the exon union file] [name of the individual transcripts file] [starting from beginning of the file, to be for how many genes, default: the whole file]`