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Search: Posts Made By: JackieBadger
Forum: Bioinformatics 04-27-2015, 08:07 AM
Replies: 5
Views: 2,114
Posted By JackieBadger
This will do it https://code.google.com/p/jmhc/

This will do it https://code.google.com/p/jmhc/
Forum: Academic/Non-Profit Jobs 04-15-2015, 09:37 AM
Replies: 0
Views: 687
Posted By JackieBadger
Paid internship to model MHC evolution

We are looking for an undergraduate to undertake a paid internship this summer at the University of East Anglia, UK, to implement a novel model of MHC evolution, which we are developing.

Info, and...
Forum: Bioinformatics 02-03-2015, 01:58 AM
Replies: 4
Views: 2,955
Posted By JackieBadger
FactoR mine is essentially performing independent...

FactoR mine is essentially performing independent comparisons among the data here like one would with a correlation coefficient or regression. Strictly speaking it is not giving a P value for the...
Forum: Bioinformatics 10-30-2014, 10:43 AM
Replies: 4
Views: 1,469
Posted By JackieBadger
Upload your data to Galaxy https://usegalaxy.org ...

Upload your data to Galaxy https://usegalaxy.org
Use FASTA manipulation to convert from FASTA to tabular.

You may then need to use the Text Manipulation tool to rearrange your columns.
Forum: Ion Torrent 09-28-2014, 03:06 AM
Replies: 0
Views: 1,270
Posted By JackieBadger
Quick and easy question about Ion Torrent

Hi,

Probably a simple answer but I can't seem to find it.

How many cycles does the Ion Torrent workflow implement during emulsion PCR?

Cheers,

J
Forum: General 08-20-2014, 03:02 PM
Replies: 16
Views: 4,195
Posted By JackieBadger
Where did I dismiss something that I don't...

Where did I dismiss something that I don't understand?
I asked you for evidence of "God". I didn't dismiss it and say I don't understand.

Of course the word supernatural has a meaning. The...
Forum: General 08-09-2014, 02:59 AM
Replies: 16
Views: 4,195
Posted By JackieBadger
But this is a scientific forum. Science deals...

But this is a scientific forum. Science deals with many issues that have social connotations. Sexuality is a huge part of biology, and homosexuality has been studied in many species. I see nothing...
Forum: Bioinformatics 07-12-2014, 01:32 AM
Replies: 6
Views: 5,100
Posted By JackieBadger
OmegaMap...

OmegaMap http://www.danielwilson.me.uk/omegaMap.html
Forum: Service Providers 07-08-2014, 01:37 AM
Replies: 14
Views: 11,043
Posted By JackieBadger
good and free (collaborative basis)...

good and free (collaborative basis) http://www.nextgenintelligence.com
Forum: Bioinformatics 07-02-2014, 04:19 AM
Replies: 3
Views: 1,314
Posted By JackieBadger
What exactly is your question? Perhaps...

What exactly is your question?


Perhaps "Why are my genotypes showing to have some heterozygosity and why are replicates not identical?"

The answer would simply be artifacts in your...
Forum: Bioinformatics 06-24-2014, 07:21 AM
Replies: 1
Views: 1,153
Posted By JackieBadger
As a follow up, if you are interested please see...

As a follow up, if you are interested please see our recent review about using NGS for de novo multigene family genotyping:

http://onlinelibrary.wiley.com/doi/10.1111/mec.12843/abstract

Thanks
Forum: Bioinformatics 04-01-2014, 06:48 AM
Replies: 9
Views: 3,744
Posted By JackieBadger
If you have a good reference you can map directly...

If you have a good reference you can map directly to it. I have done this with Newbler before and got quick and good mtDNA genomes out of total DNA pools
Forum: RNA Sequencing 03-04-2014, 06:06 AM
Replies: 4
Views: 4,735
Posted By JackieBadger
MIRA assembler can detect chimeras I believe

MIRA assembler can detect chimeras I believe
Forum: Bioinformatics 03-01-2014, 01:49 PM
Replies: 6
Views: 1,209
Posted By JackieBadger
Without knowing how many sequences you want to...

Without knowing how many sequences you want to compare, the obvious choice would be to use BLAST
Forum: Bioinformatics 03-01-2014, 12:34 PM
Replies: 6
Views: 1,209
Posted By JackieBadger
what do you mean by search? You want to...

what do you mean by search?

You want to search based on sequence similarity to known genes or search based on a known sequence identifier?
Forum: Sample Prep / Library Generation 02-27-2014, 02:37 PM
Replies: 2
Views: 2,261
Posted By JackieBadger
Without answering the your question, I can tell...

Without answering the your question, I can tell you that 120 individuals (especially with such large genomes) in one lane is out of the question. With such a large genome, 5 - 10 individuals..maybe...
Forum: General 02-25-2014, 04:53 PM
Replies: 10
Views: 2,190
Posted By JackieBadger
OK. It wasn't immediately clear that he was...

OK. It wasn't immediately clear that he was refrying to modification of bases by methylation. It will be interesting to see if we can harness this information in DNA sequencing down the road, and the...
Forum: General 02-25-2014, 03:35 PM
Replies: 10
Views: 2,190
Posted By JackieBadger
I'm sorry but I don't follow any of this. ...

I'm sorry but I don't follow any of this.

What is "the T issue"?
What evidence is there to support that there are more than five nitrogenous bases and how does PCR suppress this evidence?
What...
Forum: General 02-25-2014, 11:04 AM
Replies: 10
Views: 2,190
Posted By JackieBadger
thanks! j

thanks!

j
Forum: General 02-25-2014, 10:40 AM
Replies: 10
Views: 2,190
Posted By JackieBadger
This is what I thought. So it essentially...

This is what I thought.
So it essentially relies on being able to sequence an entire genome, or chromosome, that contains your region of interest.

What is the maximum sequence achieved thus far...
Forum: General 02-25-2014, 07:32 AM
Replies: 10
Views: 2,190
Posted By JackieBadger
How does nanopore allow targeted sequencing of large genomic regions?

An advantage boasted by oxford nanopore is that no PCR is required. However, it is not clear to me how one would target a large genomic region, say 1MB for arguments sake, without a huge PCR at a low...
Forum: Bioinformatics 02-24-2014, 10:43 AM
Replies: 0
Views: 646
Posted By JackieBadger
Annotating SNPs from mapping locational information

Hi,

We have a few thousand RAD SNPs which were characterized using a partially annotated genome.


SNP identifies look as follows. gb indicates the genome contig where the SNP is found
...
Forum: Bioinformatics 02-21-2014, 01:32 PM
Replies: 3
Views: 2,055
Posted By JackieBadger
So you essentially have a fasta file with >800k...

So you essentially have a fasta file with >800k unique sequences?

You can just use the cat or split function in linux
Forum: Bioinformatics 02-21-2014, 11:08 AM
Replies: 4
Views: 1,705
Posted By JackieBadger
You shouldn't have different numbers of reads in...

You shouldn't have different numbers of reads in R1 and R2 files. Maybe your demultiplex script is throwing some sequences out based on quality or Ns?

Are R1 and R2 derived from a targeted...
Forum: Bioinformatics 02-19-2014, 04:57 PM
Replies: 12
Views: 3,350
Posted By JackieBadger
While I only have experience estimating CNV in...

While I only have experience estimating CNV in targeted amplicons, and can't answer your question directly, I know there are at least a couple of reviews looking at CNV detection methods.

Here is...
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