You need to set it up to use hardware trigger. I’m away from a computer but can dig up some code on Monday. @kaspar may be able to help as he is working on this at the moment.
Hi,
Gilad E. contacted me with the following request:
I’m interested in using different kinds of polymerases during clustering to cluster more complex kinds of DNA with secondary structures that do not cluster on standard Illumina clustering. Do you have any information on: 1) the basic materials (syringes, ports) needed for flowing reagents in and out of the flowcell? 2) How to purchase stand-alone Illumina flow cells? 3) Info on swapping different reagents instead of Illumina reagents in the cBot instrument during clustering?
Right, so as far I can tell I can set the trigger 2 ways.
I can use dcam_settriggermode with the mode = 1 for internal or the mode = 128 for TDI.
I can use dcam_setgetpropertyvalue with the property id for trigger mode and the property value of either 1 (normal), 3 (PIV/ fast repeat mode), 7 (multigate), or 8 (multiframe).
I think I’ve tried all the different combinations. Logically, I thought it would have just been dcam_settriggermode = TDI, but I haven’t been successful.
Here is a source file circa 2008 (around the time the camera was released) where you can see how MM did it. Does that help?
I’m not sure if this is DCAM-API v4 or not. From memory there may be differences between v4 and what MM used back then. I’m on holiday but can dig harder when I get back next week. Possibly @kaspar can say something more sensible since (hopefully) he is currently working on this.
If he doesn’t want to use Illumina stage for the flow cell to world interface, I’ve plasma bonded PDMS donuts to glass flow cells to stick tubing into.
It sounds to be a good idea to try to sequence DNA that cannot be sequenced properly with the standard Illumina technology. Sometimes it is difficult to know if the problem comes from the library preparation step, the clustering step, the sequencing step or if it is a mixture of all that…
In case it may help to start with, we have here in Paris some old Illumina consumable & reagents for HiSeq2500 mainly and also MiSeq (list below)
the basic materials (syringes, ports) needed for flowing reagents in and out of the flowcell?
In the rehyb kits (TruSeq Rapid Rehybridization kit) there are seringes and capillaries to fill th flowcells
How to purchase stand-alone Illumina flow cells?
Usually not possible to buy without the reagents to do the clonal amplification
We have some old not used FlowCell (8 lanes for HiSeq2500)
Info on swapping different reagents instead of Illumina reagents in the cBot instrument during clustering?
Never try to do that…
Let me know if some of these reagents may be usefull, because it takes space in our freezers.
Finally I found out who this ominiouse Christine is. A Meeting in Paris at La Generale with Emanuel Rebus and an enlighting insight in her practice. Hope to see you again. Best to keept good contact with the people in resource. Christine is working for the Institute for rare genetic illnesses, so her offer of all the equipment leftovers is not a scam, she has great experiences.
Would be great to somehow involve here in further processes. And, Paris, Lausanne is very close.
Nice things to come. all best
Maya
