See this page in the users guide:  Personal Synonyms

Chromosome synonyms

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 exBed.bed file.  Use the "genome" load mode, the file only includes a scattering of annotations.

•  Observe that the annotations from exBed appear on the same chromosomes as the automatically loaded annotations.

If IGB creates new chromosomes labeled "KlingonChr1" etc, then the link between chromosome "KlingonChr5" and "Chr5" is not functioning.

Genome version synonyms

TBD