Let me try and understand...
Incoming file has quotes in it. You want to send it to a database. When you get it back from the database then you still want those quotes to be there.
So is it just to/from the database that you are having your issue?
If so then I highly suspect you are doing something on the order of: (I'm wrapping it in a disclaimer to keep the unsuspecting from misunderstanding and cutting/pasting into their own applications. ;))
BAD DO NOT DO THIS
String sql = "insert into foo (bar,baz) values(" +myValue1 + ", " + myValue2 + ")";
Statement stmt = connection.createStatement();
stmt.executeUpdate( sql );
BAD DO NOT DO THAT
If so then you should really be using prepared statement's parameters at a minimum. a) you will be less vulnerable to malicious garbage deleting all of your tables, and b) you will not have any escaping problems.
String sql = "insert into foo (bar, baz) values( ?, ? )";
PreparedStatement stmt = connection.prepareStatement( sql );
stmt.setString( 1, myValue1 );
stmt.setString( 2, myValue2 );
stmt.executeUpdate();
Note that it's also safer in the case of things like CLOBs and the specifics of different DB implementations (I'm thinking of you Oracle >))
If it is some other kind of escaping, ie: to/from XML or to/from HTML then that's different but well documented all over the web.
Or provide some example code if I'm totally off base.