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Disassemble Readings

This function is used to remove readings from a database or move readings to new contigs. If readings are removed from the database all reference to them is deleted. If readings are moved to new contigs each will start a new contig containing only the named reading. Such readings can then be processed by Find internal joins and the Join editor. This is useful for repositioning a reading in a repeat: once separated it can be placed in the join editor and scrolled by the other copies. The program 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.

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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.

It is also possible to interactively select batches of readings for disassembly using the Contig Editor.See section Remove Readings.


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This page is maintained by James Bonfield. Last generated on 2 Febuary 1999.
URL: http://www.mrc-lmb.cam.ac.uk/pubseq/manual/gap4_107.html