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Forum: Bioinformatics 04-23-2009, 08:45 AM
Replies: 236
Views: 586,831
Posted By bioinfosm
I think it will be a good idea to include RNA-SEQ...

I think it will be a good idea to include RNA-SEQ tools in the huge table. The one tool I know for that = erange
Forum: Bioinformatics 03-11-2009, 01:27 PM
Replies: 236
Views: 586,831
Posted By bioinfosm
LookSeq: ALignment visualization

from Sanger
http://www.sanger.ac.uk/Software/analysis/lookseq/
Forum: Bioinformatics 03-04-2009, 07:55 AM
Replies: 236
Views: 586,831
Posted By bioinfosm
SHORE (SHOrt REads)

It is an impressive package .. with a lot of statistics and pretty plots generated at the end of analysis. Wonder why no one catched it here.

http://1001genomes.org/downloads/

Now my query is,...
Forum: Bioinformatics 02-14-2009, 09:24 PM
Replies: 236
Views: 586,831
Posted By bioinfosm
Most conservative aligner

I wish to find the best alignment of my 32bp and 100bp reads (separately, not as single input), and also determine the next best matches. Which algorithm would be most suitable for this purpose?

I...
Forum: Bioinformatics 11-20-2008, 08:16 AM
Replies: 236
Views: 586,831
Posted By bioinfosm
Thanks Nils. Could you possible post your...

Thanks Nils. Could you possible post your presentation somewhere?
I probably wont get a chance to look at the tool for a while...

thanks.
Forum: Bioinformatics 11-05-2008, 01:33 PM
Replies: 236
Views: 586,831
Posted By bioinfosm
BFAST? ...

BFAST?
https://secure.genome.ucla.edu/index.php/BFAST

Anyone has experience with it?
Forum: Bioinformatics 07-16-2008, 08:11 AM
Replies: 236
Views: 586,831
Posted By bioinfosm
THere is the NextGENe from Softgenetics that...

THere is the NextGENe from Softgenetics that looks pretty good with the condensation of reads
Forum: Bioinformatics 03-24-2008, 11:21 AM
Replies: 236
Views: 586,831
Posted By bioinfosm
ace files from MAQ or SOAP alignment viewable in EagleView

Anyone tried that? Converting the MAQ or SHrimp alignment to .ace file format, which can be used in the EagleView tool from Marth Lab?

I was looking for a good way to convert alignments to .ace...
Forum: Bioinformatics 03-12-2008, 11:38 AM
Replies: 236
Views: 586,831
Posted By bioinfosm
Thanks apfejes I know of the FindPeaks tool ......

Thanks apfejes
I know of the FindPeaks tool ... the others you mention are available somewhere to download and try?

I am looking to use a few of the short read tools available to see how they...
Forum: Bioinformatics 03-12-2008, 11:18 AM
Replies: 236
Views: 586,831
Posted By bioinfosm
parsing the output

How are people making use of outputs from various tools?

For instance
soap has this one line format with its way of representing variation
shrimp seems even more complicated with a fasta line...
Forum: Bioinformatics 03-10-2008, 09:23 AM
Replies: 236
Views: 586,831
Posted By bioinfosm
GeoSpiza

Anyone heard of them? or their suite of tools for next gen data analysis, visualization and management?
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