first previous next last contents

Ruler

If more than one contig is displayed, the contigs are positioned in the same left to right order as the input contig list, which need not necessarily be in the same order as the contig selector. Overlapping contigs are drawn as staggered lines. The horizontal distance between adjacent contigs is determined from any available read pair information. In the absence of any read pair information the second contig is positioned immediately following the first contig, but will be drawn staggered in the vertical direction. If the readings on a template spanning two contigs are consistent, the distance between the contigs is determined using the templates' mean length. If there are several templates spanning a pair of contigs an average distance is calculated and used as the final offset between the contigs. Templates which span non-adjacent contigs or contain inconsistent readings are not used in the calculation of the contig offsets. It is possible that data in the database is inconsistent to such an extent that although spanning templates have consistent readings, the averaging can lead to a display which shows the templates to have inconsistent readings, eg the readings are pointing in opposite directions.

A summary of the templates and readings used to calculate the distance between two contigs is displayed in the output window. An example is given below:

============================================================
Wed 02 Apr 10:35:51 1997: template display
------------------------------------------------------------
Contig zf98g12.r1(651) and Contig zf23d2.s1(348) 
Template       zf22h7( 376) length 1893
Reading        zf22h7.r1(  +10R), pos   6257 +208, contig  651
Reading        zf22h7.s1( -376F), pos    145 +331, contig  348
Template       zf49f5( 536) length 1510
Reading        zf49f5.r1( +255R), pos   6562 +239, contig  651
Reading        zf49f5.s1( -536F), pos    227 +135, contig  348
Gap between contigs = -11
Offset of contig 348 from the beginning = 7674

The contig names and numbers are given in the top line. Below this, the spanning template name, number and length is displayed. Below this the reading name, whether the reading has been complemented (+: original -: complemented), number, primer information, starting position, length and contig number. This is of similar format to that displayed by the read pairs output.See section Find Read Pairs. The average gap between the contigs is given and finally the distance in bases between the start of the second contig and the start of the left most contig in the display.

The order of the contigs can be changed within the template display by clicking with the middle mouse button on a contig line and dragging the line to the new position. The template display will update automatically once the mouse button is released. The change of a dark yellow template to bright yellow is indicative that the two contigs are now in consistent positions and orientations. The order of the contigs in the Gap database, as displayed in the contig selector, can be updated by selecting the "Update contig order" command in the Edit menu.

By clicking on any of the contig lines in the ruler a popup menu is invoked. From this, information on the contig can be obtained, the contig editor can be started, the contig can be complemented, and the templates within the contig can be highlighted (shown by changing their line width).


first previous next last contents
This page is maintained by James Bonfield. Last generated on 2 Febuary 1999.
URL: http://www.mrc-lmb.cam.ac.uk/pubseq/manual/gap4_77.html