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Old 06-09-2011, 05:33 AM   #1
markwatson
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Default PacBio RS latest specs anyone?

Hi All

With a few units now out there has anyone got any data parametrics to share. What read lengths are you getting using each of the opration modes. Has the raw read accuracy increased? To what? We are talking in the field experience rather than company specs.

Cheers
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Old 09-16-2011, 12:14 PM   #2
myrna
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Are there even recent company specs posted anywhere?
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Old 09-16-2011, 12:54 PM   #3
GenoMax
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We are getting post-filter mean read lengths of between 1.5 - 2.0 kb and between 25-40K reads per SMRTcell. We have mainly done just standard sequencing and "filter only" analysis at the moment.


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Originally Posted by markwatson View Post
Hi All

With a few units now out there has anyone got any data parametrics to share. What read lengths are you getting using each of the opration modes. Has the raw read accuracy increased? To what? We are talking in the field experience rather than company specs.

Cheers
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Old 09-16-2011, 01:29 PM   #4
myrna
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Out of interest, how long do you have to run the machine to yield an average read length of 1.5-2kb?
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Old 09-18-2011, 01:43 AM   #5
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And what ballpark cost is it per run?
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Old 09-19-2011, 04:48 AM   #6
GenoMax
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We are doing 2 x 45 min runs, so 90 min per SMRTcell.

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Originally Posted by myrna View Post
Out of interest, how long do you have to run the machine to yield an average read length of 1.5-2kb?
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Old 09-21-2011, 12:24 PM   #7
clostridium40
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Quote:
Originally Posted by GenoMax View Post
We are getting post-filter mean read lengths of between 1.5 - 2.0 kb and between 25-40K reads per SMRTcell. We have mainly done just standard sequencing and "filter only" analysis at the moment.
What is your overall impression of PacBio RS? What are the pros and cons you have seen? If you can, how would you compare it to other technologies?
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Old 09-22-2011, 07:01 AM   #8
GenoMax
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It is a little early to say something definitive.

This is a relatively young company that is trying to succeed (the layoffs reported yesterday should give people something to think about though) in the world of Illumina/ABI.

I do not work on the "wet-bench" side of things so can't comment on how easy/difficult things are.

PacBio made some design decisions on the SMRTanalysis package ("primary" analysis happens on the cluster associated with the instrument, end-users have no access to this part) software that may or may not work for all (I suppose they had to start somewhere). This is an area that needs improvement and polish (e.g. currently no quality scores (so no fastq) can be had for sequence data by default). Hopefully these are temporary inconveniences that will be addressed in due course of time.

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What is your overall impression of PacBio RS? What are the pros and cons you have seen? If you can, how would you compare it to other technologies?
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Old 09-22-2011, 05:22 PM   #9
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Hi GenoMax

Thank you for your feedback on the software. I wanted to let you know that you can set the software to produce fastq files by default by using the RS Remote software and setting up a preference for what outputs you would like to automatically produce. One of the options provided as a checkbox is fastq.
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Old 09-23-2011, 05:39 AM   #10
GenoMax
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I was referring to the "final" sequence file produced at the end of "secondary" analysis. With SMRTanalysis v.1.2.1 this is not possible.


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Hi GenoMax

Thank you for your feedback on the software. I wanted to let you know that you can set the software to produce fastq files by default by using the RS Remote software and setting up a preference for what outputs you would like to automatically produce. One of the options provided as a checkbox is fastq.
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Old 09-23-2011, 09:23 AM   #11
pacbio
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Quote:
Originally Posted by GenoMax View Post
I was referring to the "final" sequence file produced at the end of "secondary" analysis. With SMRTanalysis v.1.2.1 this is not possible.
Thanks for the clarification. With the current version of SMRT Analysis, we offer BAM as an output which contain the consensus call QVs. To get at fastq, you will need to use post processing scripts, Picard, etc. However, we will add this feature request.

Thanks again.
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