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Search: Posts Made By: Stegger
Forum: Bioinformatics 02-11-2012, 09:53 PM
Replies: 9
Views: 3,763
Posted By Stegger
Please self-promote all you can, that just allow...

Please self-promote all you can, that just allow me to come back with potential questions to the right people :)
Forum: Bioinformatics 02-10-2012, 05:06 AM
Replies: 9
Views: 3,763
Posted By Stegger
Thanks both of you!! And Zam, I may take you...

Thanks both of you!!

And Zam, I may take you up on that offer. And congratulations on that paper.
Forum: Bioinformatics 02-09-2012, 01:13 AM
Replies: 9
Views: 3,763
Posted By Stegger
Hi Zam, I have assembled the reads into...

Hi Zam,
I have assembled the reads into contigs, and they have names_contigID to them indicating the species and specific isolate they come from. And yes, it from them that I would like to extract...
Forum: Bioinformatics 02-09-2012, 12:52 AM
Replies: 9
Views: 3,763
Posted By Stegger
Calculation of pan- and core-genome

Hi,
I was hoping someone here could point me in the direction of a good tool for calculation of pan and core genomes in prokaryotes! I am looking for one or several tools/scripts that does a number...
Forum: Bioinformatics 01-19-2012, 05:39 AM
Replies: 17
Views: 6,738
Posted By Stegger
My pleasure! and yes I had a very good...

My pleasure!
and yes I had a very good reference..
Forum: Bioinformatics 01-19-2012, 04:13 AM
Replies: 17
Views: 6,738
Posted By Stegger
Hi, I had similar NGS data on a 3 Mbp bacterial...

Hi,
I had similar NGS data on a 3 Mbp bacterial pathogen, PE and MP Illumina data, and at least with an older version of the CLC GW assembler I also got much worse results with combined assembly...
Forum: Bioinformatics 11-18-2009, 12:05 AM
Replies: 236
Views: 504,384
Posted By Stegger
Their 36 bases.

Their 36 bases.
Forum: Bioinformatics 11-17-2009, 12:12 AM
Replies: 236
Views: 504,384
Posted By Stegger
I am using the CLC Genomics Workbench on my...

I am using the CLC Genomics Workbench on my laptop running XP with 3 GB and it handle up to about 10 million Illumina reads in a de novo assembly, but things larger than that causes problems on my...
Forum: SOLiD 06-19-2009, 05:06 AM
Replies: 6
Views: 1,862
Posted By Stegger
Hi Ruby, did you tried any of the links from...

Hi Ruby,
did you tried any of the links from here: http://www.clcbio.com/index.php?id=1342

Stegger
Forum: Bioinformatics 04-02-2009, 12:41 PM
Replies: 65
Views: 29,499
Posted By Stegger
Thanks Rudy, I will try and look a bit further...

Thanks Rudy, I will try and look a bit further into my assembly output!
Forum: Bioinformatics 04-02-2009, 12:39 PM
Replies: 65
Views: 29,499
Posted By Stegger
Thats true. I have the Genomics program and are...

Thats true. I have the Genomics program and are really happy with it, but I am also mostly a molecular biologist with an interest into bioinformatics but no expert. So I like the interface and...
Forum: Bioinformatics 04-01-2009, 01:11 AM
Replies: 65
Views: 29,499
Posted By Stegger
Hi Torst, did you see any significant...

Hi Torst,
did you see any significant improvements in terms of speed in the 3.2 release from March? They stated that it was significantly faster (like 25%).
Forum: Site Announcements 03-04-2009, 02:13 AM
Replies: 9
Views: 4,155
Posted By Stegger
I agree, would be great to have a talk about...

I agree, would be great to have a talk about sequence annotation!

I will make a thread here as ECO suggested http://seqanswers.com/forums/showthread.php?p=3854#post3854

Stegger
Forum: Bioinformatics 03-04-2009, 02:11 AM
Replies: 3
Views: 3,575
Posted By Stegger
List of sequence/genome annotation tools (HELP NEEDED)!

Hi, in reply to a thread here: http://seqanswers.com/forums/showthread.php?t=819 I think it would be great to share tools for annotation of assembled genomes. I have a particular interest in...
Forum: Events / Conferences 02-20-2009, 04:26 AM
Replies: 15
Views: 9,112
Posted By Stegger
Yes, thank you!

Yes, thank you!
Forum: Illumina/Solexa 02-11-2009, 03:59 AM
Replies: 7
Views: 4,255
Posted By Stegger
Press release: ...

Press release:
http://investor.illumina.com/phoenix.zhtml?c=121127&p=irol-newsArticle&ID=1252407&highlight=
Forum: Illumina/Solexa 02-10-2009, 11:23 PM
Replies: 7
Views: 4,255
Posted By Stegger
They did not specify that and I did not ask,...

They did not specify that and I did not ask, sorry....
Forum: Illumina/Solexa 02-09-2009, 10:11 PM
Replies: 7
Views: 4,255
Posted By Stegger
I think you are right that the unblocking is the...

I think you are right that the unblocking is the central part. But they also mentioned better cooling as an important factor to obtain longer reads. The machine itself were to be called GAIIx, at...
Forum: Illumina/Solexa 02-07-2009, 04:23 AM
Replies: 7
Views: 4,255
Posted By Stegger
Update to the GAII -> GAIIx?

Hi,
In a meeting with an Illumina sales presentative yesterday I was told that Illumina was presenting an x-version of their GAII at the 10th annual Advances in Genome Biology and Technology (AGBT)...
Forum: Bioinformatics 01-22-2009, 10:46 AM
Replies: 236
Views: 504,384
Posted By Stegger
Hi, not sure if you have seen the following...

Hi,
not sure if you have seen the following link but found it through a google search:...
Forum: Bioinformatics 12-13-2008, 10:10 AM
Replies: 4
Views: 2,206
Posted By Stegger
Hi Anamika, if you look into your sig2.txt...

Hi Anamika,
if you look into your sig2.txt files I believe that you can see the raw scores which I guess you can translate into quality.
In every line you have first the lane number, then tile &...
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