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Old 06-20-2016, 10:47 AM   #41
GenoMax
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Quote:
Originally Posted by Brian Bushnell View Post


Both! I left Google and came back to JGI. So, it's at JGI.
Google's loss but good for us

We will have to count on you @Brian to see some unbiased eval of Sequel data once you get your hands on some.
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Old 06-20-2016, 12:59 PM   #42
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Originally Posted by GenoMax View Post
Google's loss but good for us
Ditto!


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Old 07-21-2016, 03:13 PM   #43
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Does anyone have information on how the Sequel data compares to the RSII? And when service providers will begin offering Sequel services?
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Old 07-22-2016, 06:09 AM   #44
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It is hard to tell but the description for this dataset seems to include verbiage about Sequel (not sure why the submitters would include that if this was a RSII): http://www.ebi.ac.uk/ena/data/view/SRX1684788

Most likely a red herring but who knows. Raw bax/bas.h5 files are available in case someone is curious (http://trace.ncbi.nlm.nih.gov/Traces...run=SRR3342814 under Download tab).

Last edited by GenoMax; 07-22-2016 at 06:21 AM.
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Old 12-11-2016, 07:20 PM   #45
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Originally Posted by Brian Bushnell View Post
No... most of what we sequence comes from remote users. But, we do all the library construction here, and I believe we reject samples that do not have high molecular weight DNA, or insufficient mass.
Hi
We are facing some issues with our new sequal system installed recently. Pacbio team is unable suggest loading clear loading concentration of different sized library.
The out put varies with each run and the maximum we got till now is 3.2gb for 2 kb library.
For the higher sized library the runs will yield 0.2-0.9gb per SMRT.We are unable to find out where the problem lies.Also after completing each run the volume of libraries pickedup from the sample well is not consistent.
Pac bio suggestion for the loading conc is 50-60pM for any size library.

There is another suggestion from PacBio is that system and smrtlink need to be restarted every 24 days, Is it true?

Please help
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Old 12-11-2016, 09:53 PM   #46
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Quote:
Originally Posted by sajeshpk View Post
Hi
We are facing some issues with our new sequal system installed recently. Pacbio team is unable suggest loading clear loading concentration of different sized library.
The out put varies with each run and the maximum we got till now is 3.2gb for 2 kb library.
For the higher sized library the runs will yield 0.2-0.9gb per SMRT.We are unable to find out where the problem lies.Also after completing each run the volume of libraries pickedup from the sample well is not consistent.
Pac bio suggestion for the loading conc is 50-60pM for any size library.

There is another suggestion from PacBio is that system and smrtlink need to be restarted every 24 days, Is it true?

Please help
I wonder if this is about recently released chemistry and software (December release) or previous one releaed October this year.
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Old 12-11-2016, 10:30 PM   #47
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Hi
The reagent version is 1.2.1 and software is SMRT Link UI 3.1.1
Change 182734 on 2016/07/07
Sajesh
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Old 12-12-2016, 04:22 AM   #48
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Originally Posted by sajeshpk View Post
There is another suggestion from PacBio is that system and smrtlink need to be restarted every 24 days, Is it true?

Please help
Welcome to the (somewhat) wacky world of PacBio.

I would suggest following all recommendations from PacBio/your FAS and keeping a good log of everything to help with troubleshooting.

A brand new technology/system needs to undergo a shakedown in real user's hands and perhaps this is just part of that process.

Last edited by GenoMax; 12-13-2016 at 05:48 AM.
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Old 12-12-2016, 02:18 PM   #49
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Further, single-molecule sequencing has lots of variables related to sample quality and sample handling. I would suggest to start with a libraries prepped from "easy and reproducible " samples like amplicons.
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Old 12-12-2016, 07:14 PM   #50
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Thanks Friends
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Old 12-15-2016, 01:05 PM   #51
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For those who may have missed it - Roche Diagnostics pulled out of their marketing agreement with PacBio: http://www.pacb.com/press_releases/p...e-diagnostics/. In the short term this means PacBio stock is cratering. In the mid- to long-term it means PacBio will have to (or 'gets to', depending on your perspective) bring a clinical version of the Sequel to market.
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Old 02-20-2017, 03:34 AM   #52
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does anybody know what service price per cell will be? is somebody who already offer service on Sequel?
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Old 02-28-2017, 10:49 AM   #53
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Here is a list of PacBio certified service providers, including those who offer services on the Sequel System: http://www.pacb.com/wp-content/uploa..._Providers.pdf
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Old 02-28-2017, 12:16 PM   #54
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I wonder if you could post a separate list for Sequel service providers.
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Old 03-30-2017, 02:07 AM   #55
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Quote:
Originally Posted by nucacidhunter View Post
I wonder if you could post a separate list for Sequel service providers.
Hi
Pls send the details on [email protected] are providing sequel services
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Old 06-15-2017, 05:32 PM   #56
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Does anybody knows how much a Pac Bio run take up in Gigabytes storage?
For example, a NextSeq Run can take up to 1.2 Tb in storage. I need this info pleaasee! jeje Thanks
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Old 06-15-2017, 05:35 PM   #57
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From what I've been told, really good PacBio runs produce about 10Gb of sequence data. I would expect that PacBio will produce less raw data than nanopore for the same sequence output, so I expect that you should be fine with about ten times that amount in space to store both sequence and raw data (i.e. 100GB).
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Old 06-16-2017, 04:44 AM   #58
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Quote:
Originally Posted by Sandra Agueros View Post
Does anybody knows how much a Pac Bio run take up in Gigabytes storage?
For example, a NextSeq Run can take up to 1.2 Tb in storage. I need this info pleaasee! jeje Thanks
We just received some Sequel data and the size of the tar files was about 20G for each cell. From past experience RSII data was ~15-25G per SMRTcell (uncompressed).
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Old 07-01-2017, 11:36 AM   #59
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Quote:
Originally Posted by nucacidhunter View Post
I wonder if you could post a separate list for Sequel service providers.
A bit late to the party, but you can find a list of Sequel providers on AllSeq.

--Shawn
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Old 09-28-2017, 01:25 AM   #60
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We have found Sequel output to be inconsistent and not sure if it is our machine. Just completed three SMRT cell runs with one library prepared for sequencing in bulk sequenced one after another but the output varies up to 125% ( 4.5, 2 and 3Gb output). I wonder if anyone have seen similar results.
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