See this page in the users guide:  Personal Synonyms

Completed in:

•  mac
•  linux
•  windows

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

•  Observe that the annotations from KlingonGenes.bed 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

Review the user guide page: Use synonyms.txt to link genome version names to each other. 

How to make the test file

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".  

1. Make an empty folder called "myQL".
2. In the myQL folder, create a plain text file called contents.txt file with this line (it is a tab between 2018 and My; do not include the bullet):
   • A_new_Jun_2018 My new genome as a test
3. In myQL, create a folder called "A_new_Jun_2018"
4. In A_new_Jun_2018, create an annots.xml file with this text:

   • <files>

       <file name="KlingonGenes.bed" title="new/KlingonGenes" />

     </files>

5. In the A_new_Jun_2018 folder, save the KlingonGenes.bed file (see Chromosome synonyms).
6. In the myQL folder, create a folder called "synsFileNotInUse"
7. In the synsFileNotInUse folder, create a text file called synonyms.txt with this text (this is two terms, separated by a tab):

• • A_thaliana_Jun_2009 A_new_Jun_2018

The synonyms file will not "work" from this location.  This is just its starting position in the test process.

How to use the test file

1. Reset preferences to give IGB a clean slate.
2. From the IGB home screen, click the species pull down. 
   •  Verify there is NO genome for "A_new"
3. Add myQL as a quickload site.
4. From the IGB home screen, click the species pull down. 
   •  Verify there IS a genome for "A_new".  
5. Select this genome, and the one genome version. 
   •  Verify that "myQL" appears in the data access list, and that you can access the KlingonGenes file (you will see Klingon chromosomes listed in the panel at the right).
6. Go to the Arabidopsis genome.  
   •  Verify that there is no myQL folder in the data access
7. Under preferences, in the data access tab, add the synonyms.txt file as a version synonyms file.
   •  IGB should prompt you to restart. Restart IGB.
   •  Verify that there is NO "A_new" genome.
   •  In the Arabidopsis genome, under data access, verify that myQL is available.
   •  Verify that you can add the KlingonGenes file in the Arabidopsis genome. You will see Klingon chromosomes listed in the panel at the right.
8. Reset preferences.
9. Move the synonyms.txt file from the synsFileNotInUse folder to the myQL folder.
10. Add the myQL quickload site.
11. Verify that
    •  There is NO "A_new" genome.
    •  The myQL folder an the KlingonGenes file are available in the data access panel in the Arabidopsis genome.