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Search: Posts Made By: RudyS
Forum: Bioinformatics 04-02-2009, 12:48 PM
Replies: 65
Views: 31,044
Posted By RudyS
objective criterion for comparing de novo assemblies

The main issue is that there is no true objective criterion for comparing de novo assemblies when no close references are available.[/QUOTE]

Torsten

For your bacterial genomes the majority of...
Forum: Bioinformatics 04-01-2009, 05:07 AM
Replies: 65
Views: 31,044
Posted By RudyS
Stegger One thing different in the new...

Stegger

One thing different in the new release is that there is no longer a minimum contig length of 200 bases ... strangely enough I am now getting "contigs" in de novo assembly of 36 bases ......
Forum: Bioinformatics 04-01-2009, 04:42 AM
Replies: 236
Views: 529,757
Posted By RudyS
xuer the browser is well documented ... suggest...

xuer
the browser is well documented ... suggest you write to the nice folks on the listserver there

[email protected]

Rudy
Forum: Bioinformatics 03-31-2009, 08:30 AM
Replies: 65
Views: 31,044
Posted By RudyS
opinions on CLC Genomics Workbench

ECO et al.

The CLC Genomics Workbench has been available for over a year and I notice that many people signed up to test it ... have people continued to use it (paying customers)? any opinions on...
Forum: De novo discovery 03-27-2009, 02:19 PM
Replies: 18
Views: 7,203
Posted By RudyS
For denovo assembly from single-end solexa reads...

For denovo assembly from single-end solexa reads are there programs that make use of the quality scores for the reads ... during the assembly decision-making process?

RudyS
Forum: Bioinformatics 03-14-2009, 07:49 AM
Replies: 236
Views: 529,757
Posted By RudyS
thanks swbarnes2 i think i will post a query...

thanks swbarnes2

i think i will post a query on the UCSC listserver
[email protected]
and see if someone like Jim Kent is thinking about some utility that could facilitate reference assembly...
Forum: Bioinformatics 03-12-2009, 06:22 PM
Replies: 236
Views: 529,757
Posted By RudyS
swbarnes are you saying that there is some...

swbarnes

are you saying that there is some utility in the UCSC Genome Browser for assembling genomes from short reads? havent heard about that ...

RudyS
Forum: Bioinformatics 03-12-2009, 09:46 AM
Replies: 236
Views: 529,757
Posted By RudyS
Staden GAP5

i note that there is no active link in the posting

* STADEN - Includes GAP4. GAP5 once completed will handle next-gen sequencing data. A partially implemented test version is available here
...
Forum: SOLiD 03-11-2009, 10:53 AM
Replies: 22
Views: 42,176
Posted By RudyS
Roald I am using CLC Genomics Workbench 3...

Roald

I am using CLC Genomics Workbench 3 ... is this already outdated considering your posting here:

"We have just included native color space assembly in our NGS Cell software"

... I have...
Forum: Bioinformatics 02-21-2009, 04:01 AM
Replies: 3
Views: 1,403
Posted By RudyS
maybe its not possible? any other de novo assembler on the horizon?

so basically its hopeless you think ... because even with paired-end reads 800-1000 base repeated elements are a long stretch? it would seem that the assembler might actually connect inappropriate...
Forum: Bioinformatics 02-20-2009, 01:22 PM
Replies: 3
Views: 1,403
Posted By RudyS
long repeated elements in a bacterial genome

if there are say 20 (almost) identical transposons of say 800 bases in a 6 Mbase genome, is there any way an assembler can properly position them using only single reads of 36 bases? and what to...
Forum: Bioinformatics 01-23-2009, 12:10 PM
Replies: 236
Views: 529,757
Posted By RudyS
likewise there is no download available on the...

likewise there is no download available on the main page
http://www.broad.mit.edu/science/programs/genome-biology/computational-rd/computational-research-and-development

though they state that it...
Forum: Site Announcements 01-15-2009, 08:29 AM
Replies: 9
Views: 4,455
Posted By RudyS
ECO i dont see much "bio" in the...

ECO

i dont see much "bio" in the bioinformatics forum ... mostly still questions about how to assemble DNA ... i did see a post from bioinfosm from almost a year ago!
1/17/08
"Just wanted to...
Forum: Site Announcements 01-15-2009, 08:28 AM
Replies: 9
Views: 4,455
Posted By RudyS
ECO i dont see much "bio" in the...

ECO

i dont see much "bio" in the bioinformatics forum ... mostly still questions about how to assemble DNA ... i did see a post from bioinfosm from almost a year ago!
1/17/08
"Just wanted to...
Forum: Site Announcements 01-14-2009, 07:32 AM
Replies: 9
Views: 4,455
Posted By RudyS
Eco Is there a separate forum for sequence...

Eco

Is there a separate forum for sequence Annotation? anybody have suggestions for (microbial) genome annotation tools to use after assembling contigs/genomes?

Thanks

RudyS
Forum: Bioinformatics 07-07-2008, 03:37 PM
Replies: 236
Views: 529,757
Posted By RudyS
STADEN - Includes GAP4. GAP5 once completed will handle next-gen sequencing data.

anybody have scoops on possible software upgrade (GAP5?) for Staden package?

hoping :)
rudy
Forum: Introductions 05-13-2008, 09:01 AM
Replies: 11
Views: 3,127
Posted By RudyS
prolly have to register to download code ......

prolly have to register to download code ... looks like "frontier" research ;)
http://euler-assembler.ucsd.edu/portal/
rudy
Forum: Bioinformatics 05-13-2008, 08:47 AM
Replies: 2
Views: 2,761
Posted By RudyS
at least some core facility support dont...

at least some core facility support dont understand the value of the prb files ... after thinking about doing what you did, i decided it didnt make sense to try to reverse-engineer the prb scores ......
Forum: Bioinformatics 05-03-2008, 09:13 AM
Replies: 22
Views: 33,696
Posted By RudyS
yuchang ::AT:: genomics.org.cn

ECO

kind fellow in canada sent me a tar file with the SOAP software with apologies for inconvenience accessing site ... will let you know what i find ... thanks for list of links
rudy
Forum: Bioinformatics 05-03-2008, 07:45 AM
Replies: 22
Views: 33,696
Posted By RudyS
cant find SOAP site in canada

this program is supposed to be available at

http://soap.genomics.org.cn

but cant access the site

i was handed a file for a resequencing project for a microcystis strain that doesnt produce...
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