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Reading and Contig Names and Numbers

For various reasons there are restrictions on the characters used in file names and the length of the file names.

Characters permitted in file names:

ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789._-

A reading name or experiment file name must not be longer than 32 characters. (In the 1997.1 releases and earlier this was limited to 16 characters.)

These restrictions also apply to SCF files which means, in turn, also to the names given to samples obtained from sequencing instruments. For example do not give sample names such as 27/OCT/96/r.1 when using and ABI machine: the / symbols will be interpreted as directory name separators on UNIX!

As each reading is entered into a project database it is given a unique number. The first is numbered 1, the second 2 and so on. Their reading names are read from the ID line in the experiment files and copied into the database. As new readings are created and existing ones removed the reading numbers change in an unpredictable fashion. Hence when taking notes on a project always record the reading name instead of the reading number.

Many options ask for a reading or contig identifier. A contig identifier is simply any reading name or number within that contig. A reading identifier is either the reading name or the hash ("#") character followed by the number. For example, if the reading name is fred.gel with number 99 users could type "fred.gel" or "#99" when asked to identify the contig.

Generally when prompting for a contig or reading name a default is supplied. This is the last name you used, or if you've only just opened the database, the name of the longest contig in the database.


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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_15.html