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Forum: Bioinformatics 03-06-2009, 04:55 AM
Replies: 22
Views: 32,525
Posted By kmay
Thumbs up Some questions...

Hi BioWizard!

Impressive number, indeed!

To better understand youir ISAS i have some questions about the background of aligning.

1) 2 point mutations: do you search exhaustively for all...
Forum: Events / Conferences 02-05-2009, 02:51 AM
Replies: 0
Views: 4,048
Posted By kmay
EMBL-Genomatix: NextGen sequencing data analysis joint workshop

>> Next Generation Sequencing is developing into a really hot topic. The
>> hardware platforms for deep sequencing are mature in the meantime,
>> however one question remains:
>>
>> How can I...
Forum: Bioinformatics 08-26-2008, 09:09 AM
Replies: 19
Views: 3,882
Posted By kmay
fabio, can I ftp your data? IŽll do a quick...

fabio,

can I ftp your data? IŽll do a quick run on them and send you the results. Will take about 15 minutes.

if it helps...

Klaus
Forum: Site Feedback/Suggestions 08-21-2008, 08:39 AM
Replies: 2
Views: 3,720
Posted By kmay
Thanks ECO for your open word! I was...

Thanks ECO for your open word!

I was "outing" myself from the beginning as a company guy and hope my postings were never felt to be too much of an advertising, though I admit a certain bias...
Forum: Bioinformatics 08-21-2008, 06:49 AM
Replies: 236
Views: 569,592
Posted By kmay
-> xxqtony: The Genomatix Mapping Station...

-> xxqtony:

The Genomatix Mapping Station could do it for you. If you can get us your data, weŽd happy to map them for you. You can see this as a test case and share your experiences here in the...
Forum: Bioinformatics 08-09-2008, 09:59 AM
Replies: 4
Views: 2,786
Posted By kmay
Hi, no fancy hardware, just an opteron...

Hi,

no fancy hardware, just an opteron processor, 2GHz
but 64GB of main memory!

->Chipper: I am travelling in the US this week. IŽll try to give you some answers later, or ask a colleague to...
Forum: Bioinformatics 08-09-2008, 04:27 AM
Replies: 236
Views: 569,592
Posted By kmay
Anthony, some Illumina real life benchmarks...

Anthony,

some Illumina real life benchmarks are posted here (http://seqanswers.com/forums/showthread.php?t=475)
Forum: Bioinformatics 08-08-2008, 09:37 AM
Replies: 4
Views: 2,786
Posted By kmay
Cool Mapping benchmarks of the GMS

Hi,

As I promised in another thread (http://seqanswers.com/forums/showthread.php?t=392) here some first controlled benchmarks from the Genomatix Mapping Station ( GMS):


Random pick of 1Mio...
Forum: Bioinformatics 08-08-2008, 02:50 AM
Replies: 10
Views: 3,626
Posted By kmay
zee, you are right. The original data were...

zee,

you are right. The original data were mapped with ELAND. At those days our GMS was under development. Later we looked at the ELAND non mapped reads and ran those over the viral genomes with...
Forum: Bioinformatics 08-07-2008, 06:33 AM
Replies: 10
Views: 3,626
Posted By kmay
Chipper, more on that with HEK cells and...

Chipper,

more on that with HEK cells and SV40 and Adenovirus is described in our paper (http://seqanswers.com/forums/showthread.php?t=447)

Klaus
Forum: Bioinformatics 08-06-2008, 09:10 AM
Replies: 10
Views: 3,626
Posted By kmay
Just a note from my side: As you know from...

Just a note from my side:

As you know from other threads, we can map from 10bp onwards, with gaps and PMs. However, before tweaking the unmapped reads into the reference genome, look at viral...
Forum: Events / Conferences 08-05-2008, 07:30 AM
Replies: 0
Views: 2,051
Posted By kmay
Genomatix Genome Analyzer on Tour in the USA

Hi yŽall !

Just wanted to let you know about some upcoming life demos of the GGA in the USA. All organized by the visited academic organizations

August 11: UMich, Ann Arbor
August 12: NYU
Aug...
Forum: Bioinformatics 08-05-2008, 07:16 AM
Replies: 14
Views: 14,120
Posted By kmay
Zee, in fact a "best unique match" search is...

Zee,

in fact a "best unique match" search is now is even faster. See the Helicos forum for some more detail on what that means. I will post some benchmarks in a couple of weeks.

Yes, we do it...
Forum: Helicos / Direct Genomics 08-05-2008, 04:05 AM
Replies: 15
Views: 16,422
Posted By kmay
Basically there was no limit on the number of...

Basically there was no limit on the number of point mutations allowed. The "unique best match" setting in our method works like that:

There is a tree with shortest unique words for each position...
Forum: Helicos / Direct Genomics 08-04-2008, 06:05 AM
Replies: 15
Views: 16,422
Posted By kmay
The raw reads were pooled from two channels. ...

The raw reads were pooled from two channels.

Again, this was a quick and dirty first pass. Mapped tag numbers can be increased significantly with more relaxed mapping parameters. However,...
Forum: Helicos / Direct Genomics 08-04-2008, 03:28 AM
Replies: 15
Views: 16,422
Posted By kmay
Okay, what I can share are numbers from our...

Okay,

what I can share are numbers from our first step analysis after mapping. Mapping was very stringent: best unique hit
(= at least one shortest unique sub-sequence contained, point mutations...
Forum: Bioinformatics 08-03-2008, 08:35 AM
Replies: 19
Views: 3,882
Posted By kmay
Fabio, before uploading the data, you have...

Fabio,

before uploading the data, you have to cluster the raw data into regions of significant tag enrichment. Annotating the raw data will most likely give you almost every gene in the genome....
Forum: Sample Prep / Library Generation 08-03-2008, 07:54 AM
Replies: 18
Views: 12,647
Posted By kmay
Chipper, I am not sure wheter I understand...

Chipper,

I am not sure wheter I understand your question right. The amplification in the wet lab amplifies everything, including unspecific noise. One should expect for later analysis that higher...
Forum: Bioinformatics 08-03-2008, 07:36 AM
Replies: 19
Views: 3,882
Posted By kmay
Dear Fabio, this question is more complex...

Dear Fabio,

this question is more complex that it seems at first glance.
When having large numbers of regions from a NGS experiment a big number of regions wonŽt fall into annotated regions....
Forum: Sample Prep / Library Generation 08-02-2008, 03:32 AM
Replies: 18
Views: 12,647
Posted By kmay
elly, sorry for having been...

elly,

sorry for having been mis-understandable!

I am talking about two steps.
1st: mapping of the reads to the genome
2nd: clustering of the mapped reads from step 1 into regions (clusters)...
Forum: Helicos / Direct Genomics 08-01-2008, 01:09 PM
Replies: 15
Views: 16,422
Posted By kmay
IŽll see

Chipper,

IŽll see what I can do. But not before next week. I cant access our secure servers from here...

Klaus
Forum: Bioinformatics 08-01-2008, 12:57 PM
Replies: 10
Views: 12,509
Posted By kmay
Hi! Glad to read that you managed the task....

Hi!

Glad to read that you managed the task. Is it from a mammalian genome? If so, would you be willing to share your data set with us ( of course NDA can be done)?
We would love to test our...
Forum: Bioinformatics 08-01-2008, 12:49 PM
Replies: 3
Views: 7,056
Posted By kmay
statistics

Hi Nix!

What are you referring to? The mapping procedures and how to detect tag-enrichment? We call this tag-clustering.
This is not published, yet but no big deal. We work with a sliding window...
Forum: Sample Prep / Library Generation 08-01-2008, 06:36 AM
Replies: 18
Views: 12,647
Posted By kmay
This low alignment rate puzzles me. elly never...

This low alignment rate puzzles me. elly never replied to this thread :(
My first guess was what apfejes took into account: was it the right reference genome? Otherwise the experiment went terribly...
Forum: Helicos / Direct Genomics 08-01-2008, 06:17 AM
Replies: 15
Views: 16,422
Posted By kmay
seen helicos data

Hi,

Helicos seems to to be so popular here ;)
Well, bells and whistles about M13 was maybe not such a wise decision...

However, I currently analyze a data set I received from Helicos. A DGE...
Showing results 1 to 25 of 29

 


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