See this page in the users guide: Personal Synonyms
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Here is an example chromosome synonyms file: chromosome.txt
KlingonChr1 Chr1
KlingonChr2 Chr2
KlingonChr3 Chr3
KlingonChr4 Chr4
KlingonChr5 Chr5
Here is an example bed file, made by taking segments from the A_thaliana_Jun_2009 gene annotations and replacing the chromosome names: KlingonGenes.bed
NovelChrom 3630 5899 AT1G01010.1 0 + 3759 5630 0 6 283,281,120,390,153,461, 0,365,855,1075,1543,1808,
KlingonChr1 5927 8737 AT1G01020.1 0 - 6914 8666 0 10 336,633,76,67,86,74,46,90,48,167, 0,509,1229,1456,1636,1834,2014,2308,2489,2643,
KlingonChr1 6789 8737 AT1G01020.2 0 - 7314 8666 0 8 280,294,86,74,46,90,48,167, 0,367,774,972,1152,1446,1627,1781,
KlingonChr1 11648 13714 AT1G01030.1 0 - 11863 12940 0 2 1525,380, 0,1686,
KlingonChr1 23145 31227 AT1G01040.1 0 + 23518 31079 0 20
etc.
Notice that there is one entry for a chromosome (NovelChrom) that is not in the synonyms file.
As per the directions in Personal Synonyms, add this chromosome.txt file as a chromosome synonyms file. Restart IGB.
Start IGB and choose the A_thaliana_Jun_2009 genome. Load the KlingonGenes.bed file. Use the "genome" load mode, the file only includes a scattering of annotations.
If IGB creates new chromosomes labeled "KlingonChr1" etc, then the link between chromosome "KlingonChr5" and "Chr5" is not functioning.
Review the user guide page: Use synonyms.txt to link genome version names to each other.
These instructions are a work in progress. You can download the test file I made: myQL
Unzip that folder, and continue to How to use the test file.
The instructions here should be viewed as a "fall back".
<files>
<file name="KlingonGenes.bed" title="new/KlingonGenes" />
</files>
The synonyms file will not "work" from this location. This is just its starting position in the test process.