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Forum: Illumina/Solexa 11-08-2011, 03:07 AM
Replies: 14
Views: 7,338
Posted By AlexB
So how then are labs dealing with the data flow?...

So how then are labs dealing with the data flow? They let users get their data on usbsticks or do they require to send them over the network?
Then the users most likely need to upload their data to...
Forum: 454 Pyrosequencing 10-30-2011, 11:27 AM
Replies: 15
Views: 4,748
Posted By AlexB
We did our first 16-plex large plasmids (~100kb...

We did our first 16-plex large plasmids (~100kb each) in 1/2 a XL+ run and are very happy with the data (both lenght, quality and coverage). Depending on sequence composition of course we get nice...
Forum: Illumina/Solexa 10-30-2011, 03:31 AM
Replies: 14
Views: 7,338
Posted By AlexB
Crap! Expected the MiSeek to be running native...

Crap! Expected the MiSeek to be running native linux.....
We'll have one very soon.....have to rethink data push/pull mechanism to our server for primary QC and data sharing...
Forum: 454 Pyrosequencing 09-08-2011, 11:39 PM
Replies: 30
Views: 21,917
Posted By AlexB
Like the earlier post of jvhaarst in this thread...

Like the earlier post of jvhaarst in this thread the installer works just fine in recent ubuntu x64 versions. Make sure you can use a gui (remote or local xserver).
Apply the fixes listed here also...
Forum: 454 Pyrosequencing 05-11-2010, 12:30 PM
Replies: 2
Views: 3,590
Posted By AlexB
Thumbs up Thanks. Missed that one. Exact what I was looking...

Thanks. Missed that one. Exact what I was looking for! :D
Forum: 454 Pyrosequencing 05-07-2010, 11:53 AM
Replies: 2
Views: 3,590
Posted By AlexB
Cool Filtering clonal reads

Hey,

we are rather new to the sequencing scene and have a couple of datasets generated by different platforms of our bacterial genomes. The platforms include "older" FLX, Titanium paired...
Forum: Bioinformatics 11-16-2009, 02:55 AM
Replies: 4
Views: 6,217
Posted By AlexB
Hi It depends on what you exactly want to view!...

Hi
It depends on what you exactly want to view!
If you want to view annotations...have a look at the Artemis viewer from Sanger. That will do the job.
If you want to use BLAST/BLAT for bigblast...
Forum: Bioinformatics 10-04-2009, 11:17 PM
Replies: 10
Views: 4,999
Posted By AlexB
Thanks Torst this was exact the information we...

Thanks Torst
this was exact the information we were looking for.
Although we have a concern faclity with an older and a new 454 machine.....pricing seems very competitive at other core labs but...
Forum: Bioinformatics 10-01-2009, 06:13 AM
Replies: 10
Views: 4,999
Posted By AlexB
Arrow Current status de novo assembly 454 vs Solexa

Hi All,
We are fairly :rolleyes: new to the nextgen seq technology and when we started our bacterial genomes the companies providing sequencing opportunities were unable to do de novo assembly of...
Forum: Bioinformatics 10-01-2009, 06:03 AM
Replies: 13
Views: 42,297
Posted By AlexB
Hi Dave, what I did for our bacterial genomes...

Hi Dave,
what I did for our bacterial genomes is similar to your suggestion. Just counted the number of contrib sequences to each base in the consensus. I then read this list into Artemis for...
Forum: 454 Pyrosequencing 09-16-2009, 12:22 PM
Replies: 6
Views: 6,002
Posted By AlexB
I have to admit :o that in such detail we never...

I have to admit :o that in such detail we never looked so I can't comment. Since we were relatively new to the technology at the time we compared the results of gsmapper to the ones returned by BLAT...
Forum: General 09-15-2009, 11:13 AM
Replies: 3
Views: 1,853
Posted By AlexB
We have used so-called vectorette system in the...

We have used so-called vectorette system in the past quite succesfully. Works well on bacterial as well as eukaryotic DNA.
Our protocol that time:...
Forum: 454 Pyrosequencing 09-15-2009, 11:05 AM
Replies: 6
Views: 6,002
Posted By AlexB
Wink Maybe silly but I simply did a BLAT analysis of...

Maybe silly but I simply did a BLAT analysis of the reads (which is really fast) to a reference genome which allowed me to simply choose any cut-off I like (length as well as sensitivity %homology)....
Forum: 454 Pyrosequencing 09-12-2009, 02:07 PM
Replies: 21
Views: 28,892
Posted By AlexB
Hey the same here for me (in the Netherlands)....

Hey
the same here for me (in the Netherlands). I didn't even ask for the software but since our University already had an older (GLX) one and now have a Titanium..... They just asked whether the...
Forum: 454 Pyrosequencing 09-11-2009, 02:38 AM
Replies: 4
Views: 3,901
Posted By AlexB
quant coverage

Thanks flxlex,
good suggestions. I indeed intended tolok at the assembly and coverage of that specific contigs. I just find the numbers for repeats so high. In the latter 800 fold coverage was a...
Forum: 454 Pyrosequencing 09-10-2009, 10:47 AM
Replies: 4
Views: 3,901
Posted By AlexB
coverage quantitative?

Hi kmcarr,
yes indeed its a bacterial (streptococcus) genome. I guess that since for transcriptomics the technique is quantitative so my guess it should be for genomes as well. Just wondered whether...
Forum: 454 Pyrosequencing 09-10-2009, 06:38 AM
Replies: 4
Views: 3,901
Posted By AlexB
Question How quantitative is contig coverage?

Hi All,
I am working on draft (resequencing) genomes of about 2Mb. In one run we multiplexed three strains and that works quite ok (as far as i can see now).
I noticed one thing which I find odd...
Forum: Introductions 09-10-2009, 06:30 AM
Replies: 0
Views: 1,375
Posted By AlexB
Talking Hello from Lelystad, The Netherlands

Hi All,
I am molecular biologist+bioinformatician at the CVI in Lelystad (most focus on animal/human pathogens).
I am fairly new to next gen sequencing but currently more and more involved in de...
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