MiSeq - Page 3

james hadfield · 02-21-2011, 03:47 AM

avilella & genlyai: The price per base is much higher on MiSeq than HiSeq but the ability to get a result in 1 day vs 8 i imporatnat in many areas. I also find that users who wnat a long run often wait longer than usual as we do fewer long runs compared to SE36 for instance. In this case the 1vs8 days might be more like 1vs30 in reality. Almost certainly worth the extra cost in that instance.

james hadfield · 02-21-2011, 03:53 AM

Vinz: The MiSeq completes a PE100 run in 1 day compared to 8 on HiSeq and 12 on GAIIx. If you look at intensities and then error profiles for runs they drop off at the end. Much of this is due to the time the reagents sit on the instrument and Illumina only support ten days.
MiSeq runs fast, very fast. I am hoping that this has an impact on quality and would not be surprised to see users publishing 200, 300 and even higher read lengths. Lets wait and see when people get hold of them.

nickloman · 02-21-2011, 03:55 AM

Wow, that's an interesting thought!

Vinz · 02-21-2011, 04:14 AM

Thanks James for your thoughts! I hope you are right - a little above 200 bases would be just perfect for our application.

ECO · 02-21-2011, 09:20 AM

Quote:

Originally Posted by james hadfield

Vinz: The MiSeq completes a PE100 run in 1 day compared to 8 on HiSeq and 12 on GAIIx. If you look at intensities and then error profiles for runs they drop off at the end. Much of this is due to the time the reagents sit on the instrument and Illumina only support ten days.
MiSeq runs fast, very fast. I am hoping that this has an impact on quality and would not be surprised to see users publishing 200, 300 and even higher read lengths. Lets wait and see when people get hold of them.

I would guess that the decay of phasing and overall efficiencies would be a bigger limitation than reagent stability. Even at >99% efficiency, for 100++ sequential chemical reactions the intensities (sum of successful incorporations) and signal-to-noise (ratio of correct incorp to all three incorrect) would drop accordingly.

james hadfield · 02-22-2011, 05:02 AM

The data we saw at AGBT on longer reads showed lots of high quality data coming of the instruments. Quality is affected by many things, phasing and chemistry stability being two. I am sure reads will get longer. They have on almost every other sequencing platform over the last 30 years.

I'd be happy to do the ultra-long MiSeq experiment if only Illumina would drop one off for a long weekend.

dcfargo · 04-21-2011, 09:27 AM

Anyone have an estimate for the total size per run of the outfiles. For example a per year per machine storage need? Are the outfiles the same as the HiSeq (just much smaller)?

vebaev · 04-21-2011, 09:32 AM

Hi,
It is shown that MiSeq will be able to do smallRNAs and Chip-seq

1.I was wandering how many M clean reads will be output from the small RNA run?
2.and also is it posible to do a DGE analysis and target gene seq, on MiSeq, and overall what other application will be able to do on the platform except the mentioned above?

razibus · 05-19-2011, 08:12 AM

Quote:

Originally Posted by dcfargo

Anyone have an estimate for the total size per run of the outfiles. For example a per year per machine storage need?

You can have no more than 15 runs on the machine. Keep in mind that you will have probably to buy a computer dedicated to the MiSeq.

protist · 05-19-2011, 08:39 AM

Check out the archived Webinar for a detailed overview - http://www.illumina.com/events/webinars.ilmn

My Sample. My Study. MiSeq. Introducing Illumina's personal sequencing system (Wednesday, April 20, 2011).

krobison · 05-19-2011, 06:45 PM

Quote:

Originally Posted by razibus

You can have no more than 15 runs on the machine.

15 runs of what sort in what timeframe? Given that the instrument's longest running mode is spec-ed at about 3 days, you should be able to get more like 100 runs a year; the shorter running modes could be multiple per day.

ScottC · 05-19-2011, 07:28 PM

Quote:

Originally Posted by krobison

15 runs of what sort in what timeframe? Given that the instrument's longest running mode is spec-ed at about 3 days, you should be able to get more like 100 runs a year; the shorter running modes could be multiple per day.

Probably 15 runs total stored on the machine. I.e. the disk capacity is probably large enough to store 15 runs (i.e. time period is not relevant).

Cheers,

Scott.

razibus · 05-20-2011, 12:55 AM

Sorry but I don't have the details, they told me 10-15 runs. The device is not on the market so it is as hard to have information on MiSeq as to talk about PGM on this forum...

The main idea is that the integrated analysis module on MiSeq won't be too powerfull, for example you cannot launch a run and make your bioinformatics on an old run in the same time. That's why they are working on a solution to link MiSeq to a computer in order to transfer datas easily for example.

This is quite predictable as both GS Junior and PGM have a dedicated computer.

krobison · 05-20-2011, 10:15 AM

Quote:

Originally Posted by krobison

15 runs of what sort in what timeframe? Given that the instrument's longest running mode is spec-ed at about 3 days, you should be able to get more like 100 runs a year; the shorter running modes could be multiple per day.

DUH! Thanks for the correction.

ECO · 05-20-2011, 11:28 AM

Quote:

Originally Posted by razibus

The device is not on the market so it is as hard to have information on MiSeq as to talk about PGM on this forum...

Quote of the day.

razibus · 05-20-2011, 01:45 PM

Ok, it was too easy. No comment.

razibus · 05-24-2011, 02:31 AM

Quote:

Originally Posted by krobison

15 runs of what sort in what timeframe? Given that the instrument's longest running mode is spec-ed at about 3 days, you should be able to get more like 100 runs a year; the shorter running modes could be multiple per day.

I have the exact information now : you can have 5 runs of 6 GB on your MiSeq.

ECO · 05-24-2011, 08:13 AM

krobison has a new post up that has real information about MiSeq specs from a poster at CSHL.

Any chance of putting the poster up?

krobison · 05-26-2011, 07:45 AM

The poster & a PowerPoint deck with a smidge of additional information (for example, showing the mean quality score vs. base position) are up on the MiSeq site; only because of Anthony Fejes' post did I realize this (feeling a bit dumb I didn't look there).

You do need to do a brief leaving of name, email, etc. I suspect it does not vet your entries, so those wishing to remain anonymous can leave "bsimpson@springfield.elementary.edu" :-)

james hadfield · 05-27-2011, 02:14 PM

Hi All,

I just started blogging and my first post is about what we might get one day from MiSeq. I estimated 25Gb from a run. Sounds crazy? Check out my reasoning here...http://bit.ly/lRUwSC.

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02-21-2011, 03:47 AM	#41
james hadfield Moderator Cambridge, UK Community Forum Location: Cambridge, UK Join Date: Feb 2008 Posts: 221	avilella & genlyai: The price per base is much higher on MiSeq than HiSeq but the ability to get a result in 1 day vs 8 i imporatnat in many areas. I also find that users who wnat a long run often wait longer than usual as we do fewer long runs compared to SE36 for instance. In this case the 1vs8 days might be more like 1vs30 in reality. Almost certainly worth the extra cost in that instance.

02-21-2011, 03:53 AM	#42
james hadfield Moderator Cambridge, UK Community Forum Location: Cambridge, UK Join Date: Feb 2008 Posts: 221	Vinz: The MiSeq completes a PE100 run in 1 day compared to 8 on HiSeq and 12 on GAIIx. If you look at intensities and then error profiles for runs they drop off at the end. Much of this is due to the time the reagents sit on the instrument and Illumina only support ten days. MiSeq runs fast, very fast. I am hoping that this has an impact on quality and would not be surprised to see users publishing 200, 300 and even higher read lengths. Lets wait and see when people get hold of them.

02-21-2011, 03:55 AM	#43
nickloman Senior Member Location: Birmingham, UK Join Date: Jul 2009 Posts: 356	Wow, that's an interesting thought!

02-21-2011, 04:14 AM	#44
Vinz Member Location: Germany Join Date: Dec 2010 Posts: 80	Thanks James for your thoughts! I hope you are right - a little above 200 bases would be just perfect for our application.

02-22-2011, 05:02 AM	#46
james hadfield Moderator Cambridge, UK Community Forum Location: Cambridge, UK Join Date: Feb 2008 Posts: 221	The data we saw at AGBT on longer reads showed lots of high quality data coming of the instruments. Quality is affected by many things, phasing and chemistry stability being two. I am sure reads will get longer. They have on almost every other sequencing platform over the last 30 years. I'd be happy to do the ultra-long MiSeq experiment if only Illumina would drop one off for a long weekend.

04-21-2011, 09:27 AM	#47
dcfargo Member Location: Chapel Hill Join Date: Aug 2008 Posts: 22	Anyone have an estimate for the total size per run of the outfiles. For example a per year per machine storage need? Are the outfiles the same as the HiSeq (just much smaller)?

04-21-2011, 09:32 AM	#48
vebaev Senior Res. Location: Plovdiv, Bulgaria Join Date: Oct 2008 Posts: 110	Hi, It is shown that MiSeq will be able to do smallRNAs and Chip-seq 1.I was wandering how many M clean reads will be output from the small RNA run? 2.and also is it posible to do a DGE analysis and target gene seq, on MiSeq, and overall what other application will be able to do on the platform except the mentioned above?

05-19-2011, 08:39 AM	#50
protist Senior Member Location: Ireland Join Date: Jan 2009 Posts: 101	Check out the archived Webinar for a detailed overview - http://www.illumina.com/events/webinars.ilmn My Sample. My Study. MiSeq. Introducing Illumina's personal sequencing system (Wednesday, April 20, 2011).

05-20-2011, 12:55 AM	#53
razibus Member Location: France Join Date: May 2011 Posts: 25	Sorry but I don't have the details, they told me 10-15 runs. The device is not on the market so it is as hard to have information on MiSeq as to talk about PGM on this forum... The main idea is that the integrated analysis module on MiSeq won't be too powerfull, for example you cannot launch a run and make your bioinformatics on an old run in the same time. That's why they are working on a solution to link MiSeq to a computer in order to transfer datas easily for example. This is quite predictable as both GS Junior and PGM have a dedicated computer.

05-20-2011, 01:45 PM	#56
razibus Member Location: France Join Date: May 2011 Posts: 25	Ok, it was too easy. No comment.

05-24-2011, 08:13 AM	#58
ECO --Site Admin-- Location: SF Bay Area, CA, USA Join Date: Oct 2007 Posts: 1,358	krobison has a new post up that has real information about MiSeq specs from a poster at CSHL. Any chance of putting the poster up?

05-26-2011, 07:45 AM	#59
krobison Senior Member Location: Boston area Join Date: Nov 2007 Posts: 747	The poster & a PowerPoint deck with a smidge of additional information (for example, showing the mean quality score vs. base position) are up on the MiSeq site; only because of Anthony Fejes' post did I realize this (feeling a bit dumb I didn't look there). You do need to do a brief leaving of name, email, etc. I suspect it does not vet your entries, so those wishing to remain anonymous can leave "bsimpson@springfield.elementary.edu" :-)

05-27-2011, 02:14 PM	#60
james hadfield Moderator Cambridge, UK Community Forum Location: Cambridge, UK Join Date: Feb 2008 Posts: 221	Hi All, I just started blogging and my first post is about what we might get one day from MiSeq. I estimated 25Gb from a run. Sounds crazy? Check out my reasoning here...http://bit.ly/lRUwSC.