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 KlingonGenes.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
The user guide for this, Use synonyms.txt to link genome version names to each other, is a bit unclear. I think we'll need to add a fake genome to our test quickload site and add it to a synonyms file and make IGB treats the "fake" genome as if it were a particular real one.
How to make the test file
- Make an empty folder called "myQL".
- 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
- In myQL, create a folder called "A_new_Jun_2018"
- In A_new_Jun_2018, create an annots.xml file with this text:
<files>
<file name="KlingonGenes.bed" title="new/KlingonGenes" />
</files>
- In the A_new_Jun_2018 folder, save the KlingonGenes.bed file (see Chromosome synonyms).
- In the A_new_Jun_2018 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
- From the IGB home screen, click the species pull down.
- Verify there is
- NO genome for "A_new"
- Add myQL as a quickload site.
- From the IGB home screen, click the species pull down.
- Verify there IS a genome for "A_new".
- 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.
- Go to the Arabidopsis genome.
- Verify that there is no myQL folder in the data access
- Under preferences, in the data access tab, add the synonyms.txt file as a personal 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).
- Reset preferences.
- Move the synonyms.txt file to the myQL folder.
- Add the myQL quickload site.
- 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.