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Welcome to the ExonUnion wiki!

To create a graph you simply need

1. an input file is needed with following format (Example: geneid_refGene.tsv)

   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

2. the column number of gene's unique id (0 is first column), default 0

3. the column number of the chromosomes (0 is first column), default 3

4. the number of genes to be considered for the graph, default all the genes in the file

Then simply run the command

./run_all.sh -i [your input file name] -l [number of genes, leave empty to graph the whole file] -c [chromosome's column number, leave empty for default] -g [gene's unique id column number, leave empty for default]

Make sure to be running python 3.5 or above to be able to get the desired results.

After running the command, 3 files will be created in the Results directory:

1. geneIdSorted.bedGraph: contains a sorted version of your original file
2. exonUnion.txt: contains one line per gene, and merges the exons of the transcripts of the gene
3. result.json: contains necessary information for the d3 graph

Ex:

./run_all.sh -i file.txt

This command will execute the scripts based on file.txt, graph all genes in file.txt, and assume the unique id of the gene is in the 1st col, and chromosome is in the 4th column.

For viewing your result, just reload the page found at https://alaleh1191.github.io/ExonUnion/