Trev - Introduction

Introduction

For some types of sequencing project it is convenient to view and edit the chromatogram data prior to assembly into a gap4 database (see section Gap4 Introduction), and this is the function of the program trev.

Trev displays the original trace data, its base calls and confidence values, and it allows the sequence of the trace to be edited and the left and right cutoffs to be defined. Several file formats can be read in addition to our own Experiment Files (see section Experiment File), and 'SCF' files (see section scf). Any edits made are normally saved to Experiment files, not to the chromatogram files which we regard as archival data.

A typical display from trev is shown below. It includes the trace data, the original sequence, the edited sequence, the menu bar, and the name of the sequence being edited. The left cutoff region is shown shaded.

[picture]

The trace can be scrolled using the scrollbar directly beneath the menubar. The trace can be magnified in the vertical and horizontal directions using the scale bars to the left of the trace.

The base numbers, original sequence, edited sequence, confidence values and the trace can each be switched on or off, and the font for the original and edited sequence is selectable.

The figure below shows the bases, edited bases, a histogram of the confidence values, the traces, and the Information Window which can be switched on from the View Menu.

(Click for full size image)

Trev can be used to produce postscript files of the traces so that they can be printed. The colours, line widths, etc are configurable. An example is shown in the figure below.

[picture]

Note that we strongly recommend that readings are not edited prior to assembly as it is far better to edit them when their alignment with other readings can be seen.

This page is maintained by staden-package. Last generated on 22 October 2002.
URL: http://www.mrc-lmb.cam.ac.uk/pubseq/manual/trev_unix_1.html