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Different data sources and files sometimes use different names to mean the same thing.  To ensure that data reference to the same thing can be displayed together, IGB supports the concept of genome version and chromosome name synonyms.

IGB supports two synonyms synonym file typetypes:

  • synonyms.txt - matches lists synonyms for genome version names
  • chromosomes.txt - matches chromosome namelists synonyms for sequence names

Synonym files are tab-delimited format. Each row of the file reports a list of synonyms for the same thing, with synonyms separated by tabs. A row can contain two or more columns of data. Synonyms can contain spaces or any other character except a tab.

The value listed first in each row is typically what IGB will display.

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Do this if you have an alignment file or other data file that made using with a reference genome sequence that used different names for chromosomes than what you see when you load that genome into IGB.

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  1. Open a new file in a plain text editor (such as Notepad or TextEdit).
  2. Enter the preferred IGB name (the display name) in column 1.
  3. Press TAB to insert a tab character.
  4. Enter the next synonym.
  5. Repeat step 3 and 4 until all synonyms are entered.
  6.  Save file as chromosome.txt 

How to make a synonyms.txt file

This A synonyms.txt file lists synonyms for genome versions. IGB uses this file to integrate data from multiple sources when those sources use different names for the same genome. For information about how to create a synonyms.txt file, see: Use synonyms.txt to link genome version names to each other.

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