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Forum: Sample Prep / Library Generation 04-10-2012, 10:08 AM
Replies: 18
Views: 4,969
Posted By 454newbie
Can you post a link to the supplier? sounds...

Can you post a link to the supplier? sounds interesting!
Forum: Ion Torrent 01-10-2012, 11:05 AM
Replies: 88
Views: 148,255
Posted By 454newbie
Sorry to be pedantic, but the chip in the image...

Sorry to be pedantic, but the chip in the image clearly isn't square (measures up using the high tech method of "ruler against screen" with edge ratio of 2x1.6) that aside, back to the sensor size...
Forum: Ion Torrent 01-10-2012, 06:49 AM
Replies: 88
Views: 148,255
Posted By 454newbie
What % sensors are active on the current...

What % sensors are active on the current generation of chips, and what % are occupied with beads. I thought they were still dependent on poisson distribution, so loading at < 30% of total sites.
...
Forum: Bioinformatics 09-12-2011, 08:47 AM
Replies: 16
Views: 5,158
Posted By 454newbie
Did you work out a solution for this problem? If...

Did you work out a solution for this problem? If so-could you post it?
Forum: RNA Sequencing 07-18-2011, 09:37 AM
Replies: 24
Views: 15,210
Posted By 454newbie
Has anyone had any experience using the SMARTer...

Has anyone had any experience using the SMARTer ULTRA followed by Nextera?
Forum: Illumina/Solexa 07-07-2011, 07:14 PM
Replies: 7
Views: 5,195
Posted By 454newbie
The original question was really targeted at why...

The original question was really targeted at why restriction enzymes aren't used more frequently for preparing libraries for resequencing genomes for which decent reference genomes exist. In...
Forum: Illumina/Solexa 07-05-2011, 07:12 PM
Replies: 7
Views: 5,195
Posted By 454newbie
yes-we've used fragmentase, DNAseI, Nextera. My...

yes-we've used fragmentase, DNAseI, Nextera. My question is specifically about why restriction enzymes aren't used more, particularly now that we have decent reference genomes.
Forum: Sample Prep / Library Generation 07-05-2011, 02:30 PM
Replies: 3
Views: 2,385
Posted By 454newbie
We have been using a caliper GX for the last 18...

We have been using a caliper GX for the last 18 months, mainly for routine analysis of PCR products and sequencing libraries. Performance in our hands is basically equivalent to the Agilent...
Forum: Illumina/Solexa 07-05-2011, 02:22 PM
Replies: 7
Views: 5,195
Posted By 454newbie
Restriction enzymes for genomic DNA library prep (e.g. NlaIII)

Given the cutting frequency of NlaIII and DpnII, why aren't they used for generating libraries from genomic DNA? I realize that they were originally used to obtain sequence tags for expression, but...
Forum: RNA Sequencing 06-05-2011, 11:13 AM
Replies: 7
Views: 6,468
Posted By 454newbie
Going back to a part of the original post, but...

Going back to a part of the original post, but for any RNA-seq method,

what % reads mapping to refseq would classify as a successful vs a failed run ?

20%, 40%, 60% 80%?

Assume that you...
Forum: Bioinformatics 06-02-2011, 07:44 PM
Replies: 7
Views: 3,133
Posted By 454newbie
Idiots guide to setting up Amazon instance for sequence analysis

Does anyone know of a good "how-to" on setting up an Amazon instance for sequence analysis? IN an ideal world, this would not be targeted at the uber-expert user, more at someone with middling unix...
Forum: General 06-28-2010, 01:24 PM
Replies: 3
Views: 4,662
Posted By 454newbie
Contact Andy May at fluidigm:...

Contact Andy May at fluidigm: andy.may@fluidigm.com. His group have this worked out.
Forum: The Pipeline 10-12-2009, 03:13 PM
Replies: 3
Ibm
Views: 3,649
Posted By 454newbie
The more skeptical amongst you might have noticed...

The more skeptical amongst you might have noticed that this press release (containing few/no details beyond previous, very old announcements) came out at a similar time to the announcement of the...
Forum: Sample Prep / Library Generation 10-08-2009, 08:37 PM
Replies: 10
Views: 4,915
Posted By 454newbie
thanks. that's not the part I'm working on...

thanks. that's not the part I'm working on automating. I want to automate the process after shearing. all of the standard steps including column purifications.
Any suggestions?
Forum: Sample Prep / Library Generation 10-07-2009, 11:18 AM
Replies: 10
Views: 4,915
Posted By 454newbie
Yes- I think this just uses Ampure beads in place...

Yes- I think this just uses Ampure beads in place of the gel. I'm pretty sure it should be straightforward to replace all the minelute columns with AMPure, too. automating this would be v.easy, just...
Forum: Sample Prep / Library Generation 10-06-2009, 01:54 PM
Replies: 10
Views: 4,915
Posted By 454newbie
Automating library prep for 454/GAII

I'm looking at automating library prep for both titanium and for GAII. Does anyone know of a good solution for this? I'm planning on setting up my own system, but would be interested if there are any...
Forum: 454 Pyrosequencing 06-07-2009, 11:49 AM
Replies: 0
Views: 1,787
Posted By 454newbie
UTP and emPCR

We've just had some weird results from our first 454 amplicon library run. poor bead yields at emPCR and lots of short reads. we checked DNA concentration by qPCR, but were off in concentration by...
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