Oligo Probe Design -Jiming Lab, MSU 11/9/2018

For Windows user:

1. To use Chorus software

- download and install DockerToolBox (refer to installchorus.ppt)
- download and install VirtualBox-5.1.38-122592
- download DNA sequences data in fasta filPB
2. Open kinematic (virtual box)
- skip log in
- search for chrorus-gui2 (refer to installchorus.ppt)
3. Transfer DNA sequences file to the data folder in Linux VM
4. In Linux vm
- click ChorusGUI.sh → execute → next → Genome file (load the complete DNA sequences) → input file
(load the chromosome DNA sequences → sample folder → 5’ Labeled R Primer – Default → thread
number (how many cpu) → probe length (45) → homolog (75) → dTM (10) → Next → Run → Yes (the
bar should turn green)

----------if the run is complete chorus output (len and bed file) will be located in C:/Users/<username>/
folder
5. Click ChorusPBselect.sh → execute → file → load probe → data → bed file ( e.g TAIR10_chr4.fas.bed)
→ mini distance between two probes (45) → len file (e.g TAIR10_chr4.fas.len) → Load chr → use mouse
to span chr and select region → choose color → strand (plus) → add → save → delete → do for the
second probe

6. Go to C:/Users/<username>/
- you should see the probe sequences in bed file
- open excel and drag bed file to it
- order the sequences ( 27,000 oligos – 1,500 USD)