Forum: Academic/Non-Profit Jobs
09-06-2013, 09:18 AM
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Replies: 0
Views: 5,891
Postdoc:Evolutionary Genomics:$55,000/yr
Postdoctoral Researcher: Evolutionary Genomics
A postdoctoral position is available on the evolutionary genomics of maize in the Department of Ecology, Evolution, and Organismal Biology (EEOB) at...
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Forum: General
05-15-2013, 06:31 AM
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Replies: 26
Views: 5,090
Cellular reprogramming
I don't know. At first glance I agree with the first response however, I believe there is some experimental medical trials where immune cells are taken out of the body, then exposed antigens from...
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Forum: General
04-22-2013, 09:27 AM
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Replies: 0
Views: 906
Genome Biology DNA Day
A bioinformatics challenge is up and posted.
Anyone else testing their skills on this? There are prizes!
...
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Forum: Academic/Non-Profit Jobs
04-17-2013, 07:22 AM
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Replies: 1
Views: 1,185
Genome Informatics Position
This position is open for another 3 days. If you are interested in a challenging career that works on tons of interesting biological questions then you should apply.
Click on the following link...
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Forum: Metagenomics
04-16-2013, 06:43 AM
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Replies: 3
Views: 3,313
In diagram form.
Take all raw read files ->...
In diagram form.
Take all raw read files -> Trinity assembly program -> assembled scaffolds
take each raw reads -> align using GSNAP alignment program to assembled scaffolds -> SAM output
take...
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Forum: Metagenomics
04-15-2013, 09:49 AM
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Replies: 3
Views: 3,313
metatranscriptome
To get a proper answer you will need to provide a lot more information about how deep the sequences was, if this is an environmental sample or sterilized a with reference bacteria added, and how many...
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Forum: Core Facilities
04-11-2013, 07:18 AM
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Replies: 7
Views: 3,807
Specialization
Most researchers are specialists in their field and study a very specific question, hopefully something they find full filling and fits within the grant they wrote and was funded.
As managers of...
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Forum: Core Facilities
04-09-2013, 04:39 AM
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Replies: 7
Views: 3,807
faculty
I have found most faculty come with a biological question they would like to answer. Based on the question they have, I recommend the best platform that will meet their needs and then tell them what...
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Forum: Core Facilities
04-09-2013, 04:36 AM
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Replies: 7
Views: 3,807
50bp SE
Fair enough, If you have an organism that is very well annotated AND the organism has minimal repetitive DNA or large homologous gene families that you are interested in then yes 50bp PE data would...
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Forum: Core Facilities
04-07-2013, 05:58 AM
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Replies: 7
Views: 3,807
Running a Core
I will answer your question indirectly as a core's best practices are meant to minimize conflict between a core and its users. I started my core in September of 2011. Here is what I have discovered...
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Forum: Academic/Non-Profit Jobs
03-21-2013, 01:06 PM
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Replies: 1
Views: 1,185
NGS Data Analyst at Iowa State University
The Genome Informatics Facility at Iowa State University is seeking a motivated bioinformatics analyst, Assistant Scientist II or III, who is interested in solving challenging and interesting...
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Forum: Bioinformatics
03-14-2013, 12:42 PM
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Replies: 2
Views: 1,072
make options
Did you specify your MPICXX during compile?
make PREFIX=`pwd` MAXKMERLENGTH=99 MPICXX='/shared/openmpi/intel/bin/mpicxx'
also I use mpirun -np numberofcpu
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Forum: Literature Watch
03-14-2013, 11:43 AM
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Replies: 29
Views: 22,730
Install Error
when I follow your suggestion with the developmental version I get the following errors
icpc: command line warning #10159: invalid argument for option '-std'
CXX...
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Forum: Literature Watch
03-14-2013, 09:28 AM
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Replies: 29
Views: 22,730
read-write checkpoints
So when you say it is fixed in the developers version does that mean the read-write checkpoints will go beyond the scaffolding process?
Thanks
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Forum: Literature Watch
03-14-2013, 07:39 AM
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Replies: 29
Views: 22,730
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Forum: Literature Watch
03-13-2013, 11:01 AM
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Replies: 29
Views: 22,730
command
mpirun -np 256 Ray-v2.1.0/Ray -k 41 -read-write-checkpoints checkpoints -one-color-per-file -search ./6b/ftp.ncbi.nih.gov/genomes/EURKARYOTES/ -search ./6b/ftp.ncbi.nih.gov/genomes/Viruses -search...
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Forum: Literature Watch
03-13-2013, 10:49 AM
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Replies: 29
Views: 22,730
lots of searching
Hi again.
I was wondering if there is a way to restart a search if the run is terminated prematurely.
I am running Ray meta with all genomes from ncbi. I have a sample that contains multiple...
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Forum: RNA Sequencing
02-27-2013, 07:53 AM
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Replies: 4
Views: 1,828
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Forum: Literature Watch
02-26-2013, 08:35 AM
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Replies: 29
Views: 22,730
Nice tool
Sebastien,
This really is a nice tool. Sorry to bombard you with so many questions but I would like to know the limitations of the tools I am using. Some of the runs I have experienced where not...
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Forum: Literature Watch
02-21-2013, 10:54 AM
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Replies: 29
Views: 22,730
estimates of composition
Thanks for the quick reply. As I am working with these features more I am curious about the following.
What does ray do with contigs and scaffolds it cannot assign to a taxon?
Are they...
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Forum: Literature Watch
02-20-2013, 01:06 PM
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Replies: 29
Views: 22,730
Ray Meta
How do I include genomes other than the bacteria that are found in the NCBI-taxonomy directory that your script generates? I could drop the fasta file into a folder however...
Is there an easy...
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Forum: Bioinformatics
02-13-2013, 04:47 PM
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Replies: 1
Views: 1,121
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Forum: Bioinformatics
02-13-2013, 07:59 AM
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Replies: 1
Views: 2,132
Stampy?
I haven't tried it yet but this program appears to do what you are asking for.
http://www.well.ox.ac.uk/project-stampy
Let me know how it works for you
Andrew
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Forum: Bioinformatics
02-11-2013, 07:04 AM
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Replies: 4
Views: 2,157
GATK best practices
I was literally just reading about that here.
http://www.broadinstitute.org/gatk/guide/topic?name=best-practices
Though not sure what is recommended for the Haplotype Caller as it is still a...
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Forum: Metagenomics
02-08-2013, 03:58 AM
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Replies: 10
Views: 5,848
Assembly
Many contigs can be assembled in a metagenome.
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