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Removing Readings

It is often desirable to completely remove a reading from a contig. When not using the editor this is typically performed using the Disassemble Readings function. See section Disassemble Readings. When using the editor, the "Remove Reading" option on the editor commands menu performs a similar task.

The command marks the reading underneath the editing cursor to be removed once the editor is quitted. Until then, the reading number in the names section of the display is shown with a dark grey background. The reading will also not be used in the calculation of the consensus. Thus, if all readings at a particular section of consensus are marked for removal the consensus sequence will be shown as dashes. Selecting the "Removing Reading" command again with the editing cursor on a reading already marked for removal will cancel the removal request. The keyboard command of Control-H may also be used as a shortcut to the "Removing Reading" command.

Once the editor has been quitted you will be asked whether you wish to disassemble the marked readings. Answering "No" will simply quit the editor as normal without removing any readings. Answering "Yes" will bring up the usual "Disassemble Readings" dialogue. The options here allow removal of all readings from this contig, or non-crucial only. A crucial reading is one that will cause this contig to be broken into two or more segments. A choice is also given as to whether the readings should be completely removed from this database, or for each reading to be placed in its own contig. Pressing "OK" now will remove the readings from the contig, breaking the contig if necessary and will quit the editor. Pressing "Cancel" will close the "Disassemble Readings" dialogue without making any changes and will not quit the editor.

At any time, quitting the editor and not disassembling the readings will leave a List (see section Lists) named "disassemble" containing the readings marked for removal. These may then be disassembled at a later stage if necessary. However the list will only be available until the next editor is quit (at which stage that editor will create its own, possibly blank, disassemble list), so make a copy if necessary.


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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_58.html