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Search: Posts Made By: severin
Forum: Academic/Non-Profit Jobs 09-06-2013, 08:18 AM
Replies: 0
Views: 5,828
Posted By severin
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...
Forum: General 05-15-2013, 05:31 AM
Replies: 26
Views: 4,902
Posted By severin
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...
Forum: General 04-22-2013, 08:27 AM
Replies: 0
Views: 876
Posted By severin
Genome Biology DNA Day

A bioinformatics challenge is up and posted.

Anyone else testing their skills on this? There are prizes!
...
Forum: Academic/Non-Profit Jobs 04-17-2013, 06:22 AM
Replies: 1
Views: 1,144
Posted By severin
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...
Forum: Metagenomics 04-16-2013, 05:43 AM
Replies: 3
Views: 3,224
Posted By severin
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...
Forum: Metagenomics 04-15-2013, 08:49 AM
Replies: 3
Views: 3,224
Posted By severin
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...
Forum: Core Facilities 04-11-2013, 06:18 AM
Replies: 7
Views: 3,679
Posted By severin
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...
Forum: Core Facilities 04-09-2013, 03:39 AM
Replies: 7
Views: 3,679
Posted By severin
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...
Forum: Core Facilities 04-09-2013, 03:36 AM
Replies: 7
Views: 3,679
Posted By severin
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...
Forum: Core Facilities 04-07-2013, 04:58 AM
Replies: 7
Views: 3,679
Posted By severin
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...
Forum: Academic/Non-Profit Jobs 03-21-2013, 12:06 PM
Replies: 1
Views: 1,144
Posted By severin
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...
Forum: Bioinformatics 03-14-2013, 11:42 AM
Replies: 2
Views: 1,016
Posted By severin
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
Forum: Literature Watch 03-14-2013, 10:43 AM
Replies: 29
Views: 22,358
Posted By severin
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...
Forum: Literature Watch 03-14-2013, 08:28 AM
Replies: 29
Views: 22,358
Posted By severin
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
Forum: Literature Watch 03-14-2013, 06:39 AM
Replies: 29
Views: 22,358
Posted By severin
I am using Ray v2.1.0. Where do I download the...

I am using Ray v2.1.0. Where do I download the developers version?

Ray --version
Ray version 2.1.0
License for Ray: GNU General Public License version 3
RayPlatform version: 1.1.0
License for...
Forum: Literature Watch 03-13-2013, 10:01 AM
Replies: 29
Views: 22,358
Posted By severin
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...
Forum: Literature Watch 03-13-2013, 09:49 AM
Replies: 29
Views: 22,358
Posted By severin
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...
Forum: RNA Sequencing 02-27-2013, 06:53 AM
Replies: 4
Views: 1,783
Posted By severin
Besides mapping to multiple locations, the sam...

Besides mapping to multiple locations, the sam file also has a header that can contain many lines and throw off your count.
Forum: Literature Watch 02-26-2013, 07:35 AM
Replies: 29
Views: 22,358
Posted By severin
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...
Forum: Literature Watch 02-21-2013, 09:54 AM
Replies: 29
Views: 22,358
Posted By severin
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...
Forum: Literature Watch 02-20-2013, 12:06 PM
Replies: 29
Views: 22,358
Posted By severin
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...
Forum: Bioinformatics 02-13-2013, 03:47 PM
Replies: 1
Views: 1,088
Posted By severin
Are you starting with Illumina reads? Have you...

Are you starting with Illumina reads? Have you thought about GATK haplotype caller? How big do you expect the CNV to be?
Forum: Bioinformatics 02-13-2013, 06:59 AM
Replies: 1
Views: 2,052
Posted By severin
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
Forum: Bioinformatics 02-11-2013, 06:04 AM
Replies: 4
Views: 2,088
Posted By severin
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...
Forum: Metagenomics 02-08-2013, 02:58 AM
Replies: 10
Views: 5,722
Posted By severin
Assembly

Many contigs can be assembled in a metagenome.
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