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Search: Posts Made By: JamesH
Forum: Service Providers 10-28-2015, 05:23 PM
Replies: 7
Views: 5,394
Posted By JamesH
There tends to be a lag between the exchange rate...

There tends to be a lag between the exchange rate change and the Aussie providers prices going up, but we still find it cheaper to sequence overseas, mostly with Novogene lately, they only do PE125...
Forum: Bioinformatics 10-14-2015, 08:01 PM
Replies: 4
Views: 2,462
Posted By JamesH
If the goal is primer design for genotypin QDD is...

If the goal is primer design for genotypin QDD is very effective http://net.imbe.fr/~emeglecz/qdd.html
Forum: Sample Prep / Library Generation 09-02-2015, 06:32 PM
Replies: 7
Views: 2,369
Posted By JamesH
Sometimes soaking dried insects in TE overnight...

Sometimes soaking dried insects in TE overnight before the extraction can help with recovery
Forum: Ion Torrent 02-26-2015, 02:59 PM
Replies: 1
Views: 2,314
Posted By JamesH
QDD (http://net.imbe.fr/~emeglecz/qdd.html)...

QDD (http://net.imbe.fr/~emeglecz/qdd.html) especially if you want to genotype them by PCR
Forum: Sample Prep / Library Generation 06-04-2014, 04:49 PM
Replies: 3
Views: 2,424
Posted By JamesH
We just use one of these: ...

We just use one of these:

http://www.ebay.com.au/itm/New-2L-Steel-Ultrasonic-Cleaner-Mechanical-Commercial-Grade-Power-60W-/150840947182?pt=AU_Jewellery_Boxes_Supplies&hash=item231ed231ee&_uhb=1
Forum: Bioinformatics 11-24-2013, 02:14 PM
Replies: 13
Views: 5,614
Posted By JamesH
I'd be inclined to go for a dual xeon machine in...

I'd be inclined to go for a dual xeon machine in that price range, you will get ECC RAM, which seems to be generally more stable because it is designed for servers/enterprise, and it will be much...
Forum: Bioinformatics 11-22-2013, 01:03 PM
Replies: 13
Views: 5,614
Posted By JamesH
I've got both of these options on my desk at the...

I've got both of these options on my desk at the moment, an i7 3930 on consumer gigabyte motherboard with 32gb RAM and a Dell workstation with dual E5 2680's and 256gb RAM, first machine cost about...
Forum: General 10-04-2013, 04:19 PM
Replies: 2
Views: 3,466
Posted By JamesH
You could give lobSTR...

You could give lobSTR http://erlichlab.wi.mit.edu/lobSTR/ a try?
Forum: General 09-19-2013, 05:10 PM
Replies: 8
Views: 3,316
Posted By JamesH
For microsatellite searching I can highly...

For microsatellite searching I can highly recommend the QDD (http://gsite.univ-provence.fr/gsite/Local/egee/dir/meglecz/QDD.html) algorithm, it doesn't use much in the way of resources and screens...
Forum: General 05-17-2013, 04:59 PM
Replies: 4
Views: 6,537
Posted By JamesH
I've never done it (speedivac RNA) but we have a...

I've never done it (speedivac RNA) but we have a speedivac in the lab and I've seen a few people try, mostly without much success (the RNA tends to end up degraded).
Forum: Academic/Non-Profit Jobs 08-13-2012, 07:42 PM
Replies: 0
Views: 2,415
Posted By JamesH
Population Genetics Post Doc Australia

3 year population genetics position at the University of Queensland, Australia.

The position will involve experimental manipulation of beetle populations, testing the effects of migration and...
Forum: Bioinformatics 07-09-2012, 04:30 AM
Replies: 3
Views: 2,324
Posted By JamesH
Assembly of long reads

A recent blog post by FlxLex, commenting on work by Sergey Koren, Michael Schatz and others, indicates that genome assemblies can be significantly improved using corrected PacBio long reads...
Forum: Bioinformatics 04-21-2012, 04:51 PM
Replies: 8
Views: 2,398
Posted By JamesH
Are you trying to find polymorphic markers so...

Are you trying to find polymorphic markers so that you can design primers and screen them in a bunch of individuals? If so this is what you're after:
...
Forum: Ion Torrent 04-18-2012, 05:23 PM
Replies: 18
Views: 9,535
Posted By JamesH
Has anyone tried this: ...

Has anyone tried this:

http://www.shimadzu.com/an/lifescience/electrophoresis/mce/multina.html

instead of the bioanalyzer or labchip?

Runs are cheaper but does anyone know if it's any good?
Forum: Bioinformatics 03-16-2012, 06:45 PM
Replies: 7
Views: 4,316
Posted By JamesH
Copy the tree and paste it into illustrator, or...

Copy the tree and paste it into illustrator, or some other vector graphics program, then you can edit it and make it look the way you want, just be sure to constrain the proportions if you re-size it!
Forum: Illumina/Solexa 03-07-2012, 02:43 PM
Replies: 82
Views: 130,281
Posted By JamesH
Roche claims there are other options if the...

Roche claims there are other options if the illumina bid fails, article at genomenweb:

http://www.genomeweb.com/sequencing/roche-claims-other-options-if-illumina-deal-fails

chairman says:
...
Forum: The Pipeline 02-26-2012, 02:56 PM
Replies: 51
Views: 183,004
Posted By JamesH
I've been thinking more about the disruption that...

I've been thinking more about the disruption that the nanopore tech could cause, there's been a bit of discussion regarding the "niche" of de novo genome assembly, and granted this will be the first...
Forum: Bioinformatics 02-14-2012, 06:33 PM
Replies: 5
Views: 2,863
Posted By JamesH
Thanks guys! I don't think you can get ECC...

Thanks guys!

I don't think you can get ECC on that MB, main reason to get it was the 8 slots! Sounds like it should be OK to use non ECC, I guess few of the folding overclockers are using ECC...
Forum: Bioinformatics 02-14-2012, 04:55 PM
Replies: 5
Views: 2,863
Posted By JamesH
Consumer RAM for NGS analysis

Now that 8GB sticks are available, and you can get socket 2011 motherboards with 8 DIMM slots, here is what I'm thinking:

G Skill 32G(4x8G) DDR3 1333 PC10600 x 2 = $590

Intel Core i7 3930K...
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