5500 Wildfire

[JPC]

Ah sorry, getting my threads mixed up!

[Zaag]

6 lanes total? The number doesn't sound right to me.

1 slide = 3 lanes

[JPC]

6 lanes total? The number doesn't sound right to me.

It's a little lower than you might like but we've seen runs like this. It equates to around 150,000 reads per panel doesn't it?

[bioits]

Got 650 million reads from a slide.

6 lanes total? The number doesn't sound right to me.

[bioits]

The actual sequencing on Wildfire is chemically the same as 5500xl provided they haven't moved the buffer locations on deck (that's easy to check).
It should work.

Buffer D is different and even for those that are same, total volume in most of the bottles are different too since WF doesn't use that much buffer.

[Zaag]

Got 650 million reads from a slide.

[JackQuist]

Hi, I need your help please.

I accidentaly ordered run cycle buffers and buffer D for solid wildfire, although we do have 5500xl only. Do you think i can use these buffers, or throw them away?
thanks.

The actual sequencing on Wildfire is chemically the same as 5500xl provided they haven't moved the buffer locations on deck (that's easy to check).
It should work.

[Brunda]

Hi, I need your help please.

I accidentaly ordered run cycle buffers and buffer D for solid wildfire, although we do have 5500xl only. Do you think i can use these buffers, or throw them away?
thanks.

[JPC]

This doesn't sound practical to me, the amplification of the WF protocol happens on the slide (as with the Illumina range) so it won't be portable to the ion chip....could you imagine using the GA protocol to make libraries for the Ion?

My understanding is that there will be an emulsionPCR free strategy on the ion, they are calling 'Avalanche' but I don't think there is a release data yet.

[Nik]

Hi,

I will be in AGBT looking at this from a different angle. Perhaps someone has link/more information please.

I run a genomics facility for CR-UK and we have GA's, HiSeq and an Ion torrent to do validation sequencing and for that it's a good little tool. The down fall is the emulation PCR. Now when something goes wrong it is pretty much back to that. It’s expensive and time consuming.

Now, if you haven't worked out what I want to do yet, I want to use the wildfire library production and its non-emulation PCR and run on my Ion torrent but I can't find any details. As academia I do not have to worry about the issues companies have with IP. So, I want to give it a go. Can anyone send me links to papers, information or help on this I will buy you a drink as AGBT.

All the best

Nik

[Zaag]

How many raw reads did you get per lane?

450 million and 400 million Total reads from the multiplex report. I think this can be higher if we find the optimal amount to load on the slide.

Can anyone tell me if Wildfire will work with standard SOLiD libraries, or even better, what the Wildfire adapter sequences are?

You can PCR the Wildfire adapters to a 5500 library so that you can run it on the wildfire. I don't know the sequence.

[SeqTruth]

Library/adapter compatibility

Can anyone tell me if Wildfire will work with standard SOLiD libraries, or even better, what the Wildfire adapter sequences are?

[Chipper]

How many raw reads did you get per lane?

[Zaag]

lane1: 240 million 0 mismatch barcode reads; 80% aligned to reference (hg19)
lane2: 200 million 0 mismatch barcode reads, 71% aligned to reference (hg19)

both lanes contained the same sample, only the amount we loaded at the slides to form colonies was higher in lane2

[Zaag]

We have one now, I'll be running an old sample this week. I will post the results.