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Search: Posts Made By: clivey
Forum: The Pipeline 02-25-2012, 12:43 AM
Replies: 51
Views: 184,169
Posted By clivey
You guys ! Tsk! What I actually said was...

You guys ! Tsk!

What I actually said was that we use a 4:1 input multiplex for each circuit. So 4 array wells per circuit. When you poisson load 4 wells, 1 gets no pores, 1 gets 1, 1 gets 2 and 1...
Forum: The Pipeline 02-25-2012, 12:31 AM
Replies: 51
Views: 184,169
Posted By clivey
BBoy. You weren't at the talk so I will clairy if...

BBoy. You weren't at the talk so I will clairy if I can.

You raise the point about parallelism a lot. What you fail to consider is speed. Not all sensing circuits are the same. On a Nanopore...
Forum: The Pipeline 02-18-2012, 04:16 PM
Replies: 51
Views: 184,169
Posted By clivey
Red face Thank you for spotting that, it's nice to meet...

Thank you for spotting that, it's nice to meet someone with insight.

C.
Forum: The Pipeline 02-02-2012, 07:51 AM
Replies: 103
Views: 140,079
Posted By clivey
No spoilers - sorry. c.

No spoilers - sorry.

c.
Forum: The Pipeline 02-02-2012, 06:18 AM
Replies: 103
Views: 140,079
Posted By clivey
Hi, Joking aside. Yesterday's PR was...

Hi,

Joking aside.

Yesterday's PR was the announcement of ONTs product launch later this year, preceded by an early access stage.

the talk abstract is out a week from Tuesday and succinctly...
Forum: The Pipeline 02-01-2012, 02:17 PM
Replies: 103
Views: 140,079
Posted By clivey
Cool Tut tut ! So cynical, and as for you...

Tut tut ! So cynical, and as for you "SillyPoint", remember I know where you live !:cool:
Forum: General 04-28-2011, 08:59 AM
Replies: 37
Views: 18,701
Posted By clivey
surely the inverse of this statement is also...

surely the inverse of this statement is also true. What applications do you need tiled short reads for that cannot be addressed with long reads (of sufficient qual).
Forum: General 04-28-2011, 08:43 AM
Replies: 37
Views: 18,701
Posted By clivey
BTW, roche at 1% growth last quarter are clearly...

BTW, roche at 1% growth last quarter are clearly struggling.
Forum: General 04-28-2011, 08:42 AM
Replies: 37
Views: 18,701
Posted By clivey
What if

Your reads were over 100kb, very accurate and you had a mountain of them ?
Forum: General 03-16-2011, 01:19 PM
Replies: 7
Views: 2,547
Posted By clivey
No

There's cost of goods and price.

As a servce business, you can charge what you like when you have a capital cash pile in the 10s of millions. At least for a while. That cash pile is decreasing...
Forum: General 03-16-2011, 12:27 PM
Replies: 7
Views: 2,547
Posted By clivey
Darn !

Wraithnot, you beat me to it - by minutes !!

Even if, in the unlikely event, it were true that it had gone and Illuminas marketing group had missed it -- I think that just shows how trite and...
Forum: Illumina/Solexa 12-13-2010, 01:26 AM
Replies: 8
Views: 5,227
Posted By clivey
[QUOTE=bioinf;30246]Hi everyone. ;) I'll be...

[QUOTE=bioinf;30246]Hi everyone. ;) I'll be presenting the "Illumina GA I" in class as a seminar subject. I've already prepared the slides, but I lack a bit of information about it. I'd appreciate if...
Forum: SOLiD 04-12-2010, 02:02 AM
Replies: 9
Views: 3,069
Posted By clivey
Image QC

Was very useful when setting up and debugging machines, chemistry and protocols at Solexa and Sanger.

Often systemic issues with the instrument showed up as easily recognisible problems in the...
Forum: Bioinformatics 04-17-2009, 02:45 AM
Replies: 13
Views: 15,664
Posted By clivey
you simply need to 'recalibrate' the score so...

you simply need to 'recalibrate' the score so that Q40 means Q40 etc. some software tools are available to do this and it is not hard to write something.
Forum: Bioinformatics 03-30-2009, 06:16 AM
Replies: 6
Views: 2,005
Posted By clivey
pebcak ?

-j6 rather than -j16 sounds pretty likely.
Forum: Bioinformatics 12-19-2008, 01:45 AM
Replies: 16
Views: 5,433
Posted By clivey
Originally Solexa provided two aligners for...

Originally Solexa provided two aligners for precisely this reason. One is Eland with a 2 error limit. The other was PhageAlign with no limit. You were thus able to force align all of the reads and...
Forum: Bioinformatics 11-24-2008, 08:21 AM
Replies: 15
Views: 6,944
Posted By clivey
sanger have it set up - talk to Tom Skelley. ...

sanger have it set up - talk to Tom Skelley.

Images are still very diagnostic of any issue with your sample or sequencer (or run). Looking at images allowed sanger to optimise their pipeline. For...
Forum: Illumina/Solexa 10-16-2008, 02:58 AM
Replies: 7
Views: 2,923
Posted By clivey
hear hear !

hear hear !
Forum: Bioinformatics 10-03-2008, 01:37 AM
Replies: 6
Views: 3,228
Posted By clivey
interesting, well - look at the X and Y...

interesting,

well - look at the X and Y corordinates of the reads , are they spatially correlated ? when you look at the images is there anything about them that wrong ? have you managed to create...
Forum: Bioinformatics 10-02-2008, 07:42 AM
Replies: 6
Views: 3,228
Posted By clivey
depends what they are. If they are polyA...

depends what they are.

If they are polyA rich - they are probably a result of image artefacts (ie not derived from templates) - often caused by flowcell edges on newer systems. Other imaging...
Forum: Illumina/Solexa 10-01-2008, 08:06 AM
Replies: 8
Views: 3,483
Posted By clivey
Not sure I understand what you mean by bias ? ...

Not sure I understand what you mean by bias ?

Is it global bias - so that say, 70% are F and 30% are R% ?

do you have a forwards and reverse strand coverage graph ?

you should see equal F...
Forum: Literature Watch 09-22-2008, 01:22 PM
Replies: 7
Views: 3,763
Posted By clivey
in fact i first saw this presented at a meeting...

in fact i first saw this presented at a meeting by Gabor about 1 year ago - which implies the data are very old. Gabor is a bit more circumspect about the meaning of the results in his associated...
Forum: Bioinformatics 08-11-2008, 04:05 AM
Replies: 4
Views: 2,818
Posted By clivey
Eland was designed to avoid having 64Gb of...

Eland was designed to avoid having 64Gb of memory. It should do about 4000 reads per second per CPU on a modern CPU so ~250 seconds.
Forum: Illumina/Solexa 07-04-2008, 04:42 AM
Replies: 4
Views: 2,919
Posted By clivey
Hi - (formerly cgb here). I set up the...

Hi - (formerly cgb here).

I set up the original as a public wiki (rather than a message board like this) paid for and sponsored by Sanger (GRL). The idea being to get people to share experiences,...
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