SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 25 of 96
Search took 0.02 seconds.
Search: Posts Made By: doxologist
Forum: Literature Watch 07-07-2009, 03:06 PM
Replies: 0
Views: 1,930
Posted By doxologist
The number two-ome

http://www.the-scientist.com/2009/07/1/17/1/

Fun article about HuGE (Human Gut Ecology) Project - self-proclaimed Watson and Crick of poop. :D
Forum: SOLiD 05-28-2009, 10:26 AM
Replies: 1
Views: 1,505
Posted By doxologist
Concatenating sequences

I'm putting together a lot of smaller sequences into one big chromosome files for Corona Lite. Does anyone who what I should use to create boundaries between the files? Would "N" or "." work?
Forum: Literature Watch 05-27-2009, 07:29 AM
Replies: 0
Views: 1,324
Posted By doxologist
SHRiMP: Accurate Mapping of Short Color-space Reads

The paper is out!
http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000386

Abstract
The development of Next Generation Sequencing technologies, capable of sequencing hundreds of...
Forum: De novo discovery 03-27-2009, 09:00 AM
Replies: 18
Views: 6,867
Posted By doxologist
thanks - looking forward to the update.

thanks - looking forward to the update.
Forum: De novo discovery 03-27-2009, 08:59 AM
Replies: 18
Views: 6,867
Posted By doxologist
Velvet is only colorspace right? I'm using...

Velvet is only colorspace right?
I'm using parts of NextGENe which incorporates some de brujin graphs...
Forum: SOLiD 03-27-2009, 08:57 AM
Replies: 35
Views: 19,539
Posted By doxologist
just for trivial conversion... decode

just for trivial conversion... decode
Forum: SOLiD 03-26-2009, 12:29 PM
Replies: 35
Views: 19,539
Posted By doxologist
csfasta --> fasta conversion

I have a fast trivial question:
what's the fastest/easier way to "decode" or convert the csfasta to fasta? I'm just doing this for a handful at a time for code-checking.

thanks in advance.
Forum: De novo discovery 03-26-2009, 12:07 PM
Replies: 18
Views: 6,867
Posted By doxologist
oops... found another useful thread with these...

oops... found another useful thread with these suggestions:

* MIRA2 - MIRA (Mimicking Intelligent Read Assembly) is able to perform true hybrid de-novo assemblies using reads gathered through 454...
Forum: De novo discovery 03-26-2009, 12:04 PM
Replies: 18
Views: 6,867
Posted By doxologist
De Novo Short Read Assembler?

I'm completely new at de novo sequencing - what are good tools to assemble from short Solexa tags?
Forum: 454 Pyrosequencing 03-24-2009, 10:12 AM
Replies: 5
Views: 3,072
Posted By doxologist
can you guys be a little more specific? what does...

can you guys be a little more specific? what does slightly different mean? 5% 10% totally different hits or the target sizes just are a little different?

thanks a bunch
Forum: Bioinformatics 03-24-2009, 10:06 AM
Replies: 0
Views: 1,045
Posted By doxologist
Condensation/Consolidation methods

Hi:

I'm testing out NextGENe and the first "consolidate" their tags to make longer tags (basically using an "anchor" 12-base sequence to "grow" their tags into longer tags). Has anyone used this...
Forum: SOLiD 03-23-2009, 04:52 PM
Replies: 12
Views: 6,416
Posted By doxologist
I think there's a confusion here between SNPs for...

I think there's a confusion here between SNPs for microarray and SNP detection from sequencing. I believe the Bioconductor packages is for the former and the people were asking for the latter.

Q:...
Forum: Introductions 03-23-2009, 11:20 AM
Replies: 5
Views: 1,838
Posted By doxologist
thanks for the info. :)

thanks for the info. :)
Forum: Literature Watch 03-20-2009, 09:51 AM
Replies: 0
Views: 1,260
Posted By doxologist
Yeast Population Genomics - Sequencing vs Tiling arrays

Two papers, one with illumina sequencing:
http://www.nature.com/nature/journal/v458/n7236/full/nature07743.html
Population genomics of domestic and wild yeasts

and one with tiling arrays:...
Forum: Introductions 03-19-2009, 07:58 AM
Replies: 5
Views: 1,838
Posted By doxologist
I second the interest in the specs. :)

I second the interest in the specs. :)
Forum: Events / Conferences 03-19-2009, 07:55 AM
Replies: 23
Views: 7,386
Posted By doxologist
They sell DVDs of their recordings... I believe...

They sell DVDs of their recordings... I believe it's a very high price. (correct me if I'm wrong)
Forum: Bioinformatics 03-09-2009, 04:22 PM
Replies: 9
Views: 2,452
Posted By doxologist
thanks... that's what I expected... just wanted...

thanks... that's what I expected... just wanted to be doubly sure. :)
Forum: Bioinformatics 03-09-2009, 03:55 PM
Replies: 9
Views: 2,452
Posted By doxologist
Thanks for the info. To be doubly sure... By...

Thanks for the info. To be doubly sure... By "color reference fasta", do you mean that you translate the tags from colorspace to FASTA FIRST and then do the matching? Or is the matching done in...
Forum: Events / Conferences 03-03-2009, 07:40 AM
Replies: 23
Views: 7,386
Posted By doxologist
BioWizard: I agree that great collaboration...

BioWizard:

I agree that great collaboration must exist between commercial and academic initiatives. It just sometimes, highly commercial talks just end up being advertisement without much...
Forum: Bioinformatics 03-03-2009, 07:35 AM
Replies: 5
Views: 1,805
Posted By doxologist
I agree... there would eventually be a few...

I agree... there would eventually be a few dominant tools for each type of information space... which would take the best algorithms and be the most data-friendly. The initiatives for common format...
Forum: Bioinformatics 03-03-2009, 07:31 AM
Replies: 9
Views: 2,452
Posted By doxologist
thanks for the info.

thanks for the info.
Forum: Bioinformatics 03-02-2009, 08:30 AM
Replies: 513
Views: 174,175
Posted By doxologist
we had a similar discussion in another thread:...

we had a similar discussion in another thread: http://seqanswers.com/forums/showthread.php?p=3505

Basically, ELAND doesn't allow for different lengths and Bowtie does.
Forum: Bioinformatics 03-01-2009, 04:59 AM
Replies: 5
Views: 1,805
Posted By doxologist
oh.. by the way... the prev recommendations is...

oh.. by the way... the prev recommendations is for data with Illumina and 454. If you want to analyze Solid data, different software must be used for colorspace. Visit the solid thread for more info...
Forum: Bioinformatics 03-01-2009, 04:58 AM
Replies: 5
Views: 1,805
Posted By doxologist
IMHO, I think method with Burrows-Wheeler...

IMHO, I think method with Burrows-Wheeler transform are now the most optimal.

Bowtie is quick and easy...
bwa in the MAQ package is more flexible and extensive.

Hope this helps. :)
Forum: Service Providers 03-01-2009, 04:54 AM
Replies: 162
Views: 120,524
Posted By doxologist
Sorry.. nevermind. Visited your site... it's...

Sorry.. nevermind. Visited your site... it's clear from the webpage. :)
Showing results 1 to 25 of 96

 


All times are GMT -8. The time now is 06:01 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2017, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO