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Forum: Bioinformatics 09-18-2013, 07:13 AM
Replies: 7
Views: 4,518
Posted By cmuletz
I would recommend using Phyloseq for additional...

I would recommend using Phyloseq for additional control over your data. It takes a bit of time to get used to using it, but has a lot more power than QIIME. I think QIIME is great for a lot of the...
Forum: Bioinformatics 09-18-2013, 06:46 AM
Replies: 7
Views: 4,518
Posted By cmuletz
Not sure if you still need help with this...

Not sure if you still need help with this question. But I bet that you would able to do this in Phyloseq that is a package in R. It gives you much more control over manipulating your dataset.
Forum: Sample Prep / Library Generation 06-20-2013, 07:13 AM
Replies: 3
Views: 4,155
Posted By cmuletz
I have been using qPCR to quantify molecules/ul...

I have been using qPCR to quantify molecules/ul of my amplicons. I have not done a test to see how close Qubit readings are to that of qPCR. I was told by lab members that qPCR is much more...
Forum: 454 Pyrosequencing 01-23-2013, 08:02 AM
Replies: 4
Views: 2,523
Posted By cmuletz
You may want to contact Beckman Coulter Genomics...

You may want to contact Beckman Coulter Genomics to see if they will be helpful. I did not end up ligating the 454 adaptor sequences, but chose to use fusion primers.
Forum: Sample Prep / Library Generation 12-06-2012, 07:29 PM
Replies: 3
Views: 4,155
Posted By cmuletz
Qubit versus qPCR

Hello,

My question relates to the use of Qubit to qPCR for quantifying your amplicon samples to equimolar ratios -- we have both a Qubit/dsDNA HS Assay Kit and qPCR/ Kapa kit in our lab to...
Forum: 454 Pyrosequencing 11-01-2012, 07:34 PM
Replies: 4
Views: 2,523
Posted By cmuletz
Fusion Primer Vs. Ligation of Adaptors

Hi all,

I was recently informed from a 454 Core Facility that "amplicon libraries do not sequence as well as libraries where the adaptors are incorporated via ligation (50-100K reads vs. 150-200K...
Forum: 454 Pyrosequencing 10-18-2012, 05:32 PM
Replies: 1
Views: 1,498
Posted By cmuletz
I forgot to mention I am using the link created...

I forgot to mention I am using the link created by a previous thread on this forum to find the facilities that have a 454 FLX http://seqanswers.com/wiki/Next_Gen_Sequencing_Service_Provider
Forum: 454 Pyrosequencing 10-18-2012, 05:28 PM
Replies: 1
Views: 1,498
Posted By cmuletz
Where sequenced, how was it, and cost?

Hi folks,

I am doing an analysis of all 454 sequencing centers in the US for costs and experience with the facility. I am more interested in metagenomic experiences, but feel free to share genomic...
Forum: Introductions 07-09-2012, 10:05 AM
Replies: 0
Views: 1,350
Posted By cmuletz
Salamander Skin Microbiome Project

Hi all. I am a Ph.D. student using a 454 GS Junior to do 16s rRNA amplicon pyrosequencing of salamander skin swabs from three species of terrestrial salamanders in the Appalachian Mountains. I am...
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