Disassembling Readings

This function is used to remove readings from a database or move readings to new contigs. There are two interfaces which allow sets of readings to be disassembled. One is to identify the readings interactively when using the Contig Editor (see section Remove Readings), and the other, described below, is available as a separate option from the main gap4 Edit menu.

If readings are removed from the database all reference to them is deleted. If a reading is moved to a new contig, the new contig will contain only that single reading. Such contigs can then be processed by Find internal joins (see section Find Internal Joins) and the Join editor (see section The Join Editor), which should reveal all the other positions at which the reading matches.

Disassembly can also distinguish between "crucial" and "non-crucial" readings: a crucial reading is defined as one that, if removed, would leave a single stranded region in the contig or cause a break in the contig. Conversely non-crucial readings are those that are entirely covered by other readings from both strands of the sequence. So if only non-crucial readings were removed the amount of single stranded data would not change. Note that when readings are removed from the database the program cleans up by moving data to fill up any holes made in its list of readings, and this will cause some high numbered readings to be given different numbers.

The set of readings to be processed can be read from a "file" or a "list" and clicking on the "browse" button will invoke an appropriate browser. If just a single reading is to be assembled choose "single" and enter the filename instead of the file or list of filenames. The "Removal mode" is either "All readings" or "Non-crucial only" which are explained above. The "task" is to "Remove readings from database" or simply "Move readings to new contigs" which means each will start a new contig. For large batches of readings this processing can be quite slow.