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Search: Posts Made By: thondeboer
Forum: Bioinformatics 08-19-2014, 03:22 PM
Replies: 3
Views: 1,973
Posted By thondeboer
I have some more information on this error. It...

I have some more information on this error.
It seems to happen with most of the package on the shedtool, but not all.
It happens to this one:
...
Forum: Bioinformatics 08-15-2014, 04:04 PM
Replies: 3
Views: 1,973
Posted By thondeboer
A little more info on this issue

I have also tried to get GALAXY to run with a POSTGRES database, since the BioLinux 8 site states there is some automatic way to get galaxy to run with postgres, but there is no information their...
Forum: Bioinformatics 08-15-2014, 03:59 PM
Replies: 3
Views: 1,973
Posted By thondeboer
Error trying to install from shedtool into Galaxy on Biolinux 8

Just got Biolinux 8 and trying to install some tools in GALAXY from the toolshed, but seeing this error in the log after I press the INSTALL button in the UI

Any ideas?

192.168.50.112 - -...
Forum: Bioinformatics 02-21-2013, 05:23 PM
Replies: 0
Views: 2,008
Posted By thondeboer
Error when uisng Freebayes VCF output with GATK SelectVariants

I am seeing this error in the VariantSelect tool when I give it the output from Freebayes:

MESSAGE: The provided VCF file is malformed at approximately line number 54: BUG: log10PError cannot be >...
Forum: Bioinformatics 01-29-2013, 05:07 PM
Replies: 22
Views: 11,457
Posted By thondeboer
Problem with VCF file produced by VarScan

I also see the problem with the + and - values for the ALT allele in the VCF produced by VarScan...

I also see "str10' appear in some of the Qual fields as well (See Below).
This does not always...
Forum: Bioinformatics 01-27-2012, 02:34 PM
Replies: 2
Views: 2,891
Posted By thondeboer
Anyone know how Snowshoes-FTD finds junction-spanning reads?

Hi,

I am trying to figure out how the gene fusion program Snowshoes-FTD finds junction spanning reads. I have the article from NAR, but it does not mention how this is done. In Figure 1, it simply...
Forum: Bioinformatics 06-24-2011, 04:48 PM
Replies: 22
Views: 31,880
Posted By thondeboer
In the SAM output that we received from a...

In the SAM output that we received from a customer (NIH) that was run using ISAS, we noticed that the names for the paired-end reads, which should be identical according to the SAM definition,...
Forum: Bioinformatics 09-03-2010, 08:12 AM
Replies: 8
Views: 2,797
Posted By thondeboer
We have finally started the beta program for...

We have finally started the beta program for Avadis NGS by Strand.
If you are interested to participate, please send me a private message here and I will add you to the list....
Forum: Bioinformatics 07-21-2010, 12:18 PM
Replies: 8
Views: 2,797
Posted By thondeboer
Just let me know you are interested and send me a...

Just let me know you are interested and send me a private message with your email address and I will send you the info once we are ready to start the beta (in about a week or so).

The NGS Module...
Forum: Bioinformatics 07-21-2010, 12:03 PM
Replies: 8
Views: 2,797
Posted By thondeboer
We are aiming and designed it for being able to...

We are aiming and designed it for being able to do hundreds, but frankly have not found these kinds of data sets but simulations are in the works...What kind of data sets do you have access to?...
Forum: Bioinformatics 07-20-2010, 08:27 PM
Replies: 8
Views: 2,797
Posted By thondeboer
Looking for Beta testers for Strand NGS module

Hi,

We at Strand Life Sciences are currently working on an application for the analysis of ChIP-SEQ, RNA-SEQ and DNA Variation data and we are looking for BETA TESTERS!

The application starts...
Forum: Bioinformatics 03-07-2010, 10:16 PM
Replies: 83
Views: 250,792
Posted By thondeboer
Will original insert size of library be in SAM file header for Mate-paired sequences?

Would the original insert size for the library be listed in any resulting sequence alignment files (SAM/BAM for instance) for mate-paired reads (typicaly 2-5 kBp) or would it list the insert size of...
Forum: Bioinformatics 04-08-2009, 03:30 PM
Replies: 513
Views: 188,373
Posted By thondeboer
Hi Ben, You can read more on our read...

Hi Ben,

You can read more on our read structure on our website and on this forum as well:

http://seqanswers.com/forums/showthread.php?t=1307
...
Forum: Bioinformatics 04-08-2009, 10:49 AM
Replies: 292
Views: 145,836
Posted By thondeboer
Is there a running list somewhere that shows...

Is there a running list somewhere that shows which programs produce (or take as input) SAM/BAM format? It would help us make a final decision in what format we should produce our mapping results for...
Forum: Bioinformatics 04-08-2009, 10:30 AM
Replies: 513
Views: 188,373
Posted By thondeboer
Hi Ben, Complete Genomics here.... Have...

Hi Ben,

Complete Genomics here....
Have you tried to use our gapped read structure yet with Bowtie? As you may know, we have quite an unusual read structure so most mapping software is not able...
Forum: Introductions 03-19-2009, 10:29 AM
Replies: 5
Views: 2,109
Posted By thondeboer
There are some more specifics in some other...

There are some more specifics in some other threads on this board.

http://seqanswers.com/forums/showthread.php?t=1307

and

http://seqanswers.com/forums/showthread.php?t=1157

You can also...
Forum: Bioinformatics 03-18-2009, 10:13 AM
Replies: 292
Views: 145,836
Posted By thondeboer
Well...The reads are independent and sometimes...

Well...The reads are independent and sometimes don't agree and this is something we need to capture so we could not just remove that information.

Is there any other way in SAM (now or future) that...
Forum: Bioinformatics 03-17-2009, 11:55 PM
Replies: 292
Views: 145,836
Posted By thondeboer
I have been looking at the SAM format to see if...

I have been looking at the SAM format to see if it is something we should consider for the output of the mapping for a genome assembly we are doing at Complete Genomics. As you may know, we have...
Forum: The Pipeline 03-05-2009, 12:20 PM
Replies: 5
Views: 4,791
Posted By thondeboer
Hi, Great to hear you are excited about our...

Hi,

Great to hear you are excited about our genome sequencing service...I hope I can answer your question here (Also check the thread here:
http://seqanswers.com/forums/showthread.php?t=644

1)...
Forum: Service Providers 02-17-2009, 10:05 AM
Replies: 162
Views: 137,085
Posted By thondeboer
Comlete Genomics sequencing service

Hi,

Although we are not taking orders yet (June 2009 is our service launch), Complete Genomics is a human sequencing service, using our own technology.

http://www.completegenomics.com
...
Forum: The Pipeline 02-08-2009, 12:06 PM
Replies: 1
Views: 3,566
Posted By thondeboer
See our data as a custom track in UCSC Genome Browser

Hi,

We have created a number of files that will allow you to see our variation and genotype data as custom tracks on the UCSC Browser.

The links will load the BED data from our site directly...
Forum: The Pipeline 02-05-2009, 06:29 PM
Replies: 1
Views: 3,566
Posted By thondeboer
Lightbulb Complete Genomics releases its first draft genome. Come get our data!

Hi,

We at Complete Genomics are proud to announce the release of our first draft sequence of a completely sequenced diploid genome and are making the raw data available to the public today!

You...
Forum: Introductions 02-02-2009, 03:46 PM
Replies: 5
Views: 2,109
Posted By thondeboer
Cool Hi from Complete Genomics!

Hi,

I'm Thon, the product manager for Bioinformatics for Complete Genomics and I will be following these threads with interest!

As you may know, we are a complete genome sequencing company that...
Forum: The Pipeline 02-02-2009, 03:40 PM
Replies: 9
Views: 5,277
Posted By thondeboer
Thumbs up Complete Genomics read structure

Hi,

The read structure of our technology is two times 5+10+10+10 = 2 x 35 = 70 bp. Due to the library construction, we only read 5 bases from one of the adapters, since there are only 12-14...
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