I'm not really familiar with arules (the package that contains the read.transactions() function), but, from the documentation (since the format parameter is set to 'single' in your example):
For the 'single' format, cols is a numeric or character vector of length two giving the numbers or names of the columns (fields) with the transaction and item ids, respectively.
So, it sounds like column 1 contains the transactions, and column two contains the item ids. They need to be specified so that the input data can be turned into transactions-class.