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Forum: Sample Prep / Library Generation 12-05-2017, 10:41 PM
Replies: 10
Views: 1,689
Posted By cbird
some suggestions: Minimize tube transfers ...

some suggestions:

Minimize tube transfers

Use the with bead method to reuse beads https://genomebiology.biomedcentral.com/articles/10.1186/gb-2011-12-1-r1

don't throw out supernatant, then...
Forum: Bioinformatics 12-05-2017, 10:30 PM
Replies: 1
Views: 947
Posted By cbird
If Schweyen, H., Rozenberg, A., & Leese, F....

If Schweyen, H., Rozenberg, A., & Leese, F. (2014) didn't make a tool, then you'll probably have to use basic command line tools to make a script. Useful commands include grep or agrep, cdhit, uniq....
Forum: Core Facilities 08-10-2014, 10:18 AM
Replies: 1
Views: 1,692
Posted By cbird
Hacking An EpMotion 5075?

We have an EpMotion 5075 and it's nearly worthless when compared to undergrads.

I want to hack the controlling software so I can program it to do what I want. I have a lot of experience with a...
Forum: Core Facilities 08-10-2014, 10:02 AM
Replies: 18
Views: 13,078
Posted By cbird
On a related note, now that I'm stuck with this...

On a related note, now that I'm stuck with this thing, I want to hack the machine so we can make it do what we want. Anybody ever hacked an epmotion? Or better yet, does anybody know what company...
Forum: Core Facilities 08-10-2014, 09:58 AM
Replies: 18
Views: 13,078
Posted By cbird
We have an epMotion 5075, and it is awful. You...

We have an epMotion 5075, and it is awful. You have very little control over the machine, the software is sophmoric. It wastes tips, can't be customized, ependorf won't let you make your own...
Forum: Sample Prep / Library Generation 08-07-2014, 10:48 AM
Replies: 3
Views: 11,774
Posted By cbird
Actually, there seems to be a difference between...

Actually, there seems to be a difference between the reagents used. The AMPure XP reagent is 20% PEG in 2.5M NaCl. I do not know what the SPRI solution is (perhaps a different concentration of...
Forum: Illumina/Solexa 10-18-2013, 12:15 AM
Replies: 28
Views: 14,225
Posted By cbird
Gana, your problem probably started with the use...

Gana, your problem probably started with the use of the NanoDrop right at the beginning when you were determining how much DNA to digest. Use a fluorescent plate reader to quant your DNA.

Also,...
Forum: Sample Prep / Library Generation 10-17-2013, 11:10 PM
Replies: 49
Views: 65,903
Posted By cbird
We've found SPRI Select is much more effective...

We've found SPRI Select is much more effective than Ampure XP for size selection also. Anybody know what the difference is? I seriously doubt it's the beads themselves...

Check out this paper. ...
Forum: Sample Prep / Library Generation 10-17-2013, 10:52 PM
Replies: 46
Views: 20,306
Posted By cbird
Captainentropy, We've been working on size...

Captainentropy,

We've been working on size selection in my lab.

SpriSelect works much better than the ampure xp beads for size selection. I'm not sure why this is. I'm trying to track down...
Forum: Illumina/Solexa 05-20-2012, 10:49 AM
Replies: 15
Views: 5,627
Posted By cbird
possible explanation

I'm a novice, but I think that high cluster densities could lead to successful reads of your target DNA and unsuccessful reads of your indexes.

The Illumina sequencers use the first few...
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