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Forum: Bioinformatics 11-08-2014, 05:37 AM
Replies: 123
Views: 46,012
Posted By thomasvangurp
The server is offline, which makes tablet...

The server is offline, which makes tablet unusable. Could you please disable the requirement for loading the update server on startup?
EDIT: the issue can be fixed by referring to a non existing...
Forum: Illumina/Solexa 10-03-2014, 05:18 AM
Replies: 2
Views: 1,137
Posted By thomasvangurp
Recalibrating phasing/prephasing after run

I've recently obtained one lane PE100 Hiseq data from a highly biased library due to recstriction enzyme overhangs in reads (GBS protocol). Quality values are low for the first 10 cycles, probably...
Forum: Academic/Non-Profit Jobs 07-03-2013, 06:44 AM
Replies: 0
Views: 1,516
Posted By thomasvangurp
Thumbs up Experienced bioinformatician

Bioinformatician (embedded)
Sequencing is becoming a major technique in ecology and in the life sciences in general. The second and third generation sequencing platforms produce more data and the...
Forum: Bioinformatics 03-27-2013, 07:30 AM
Replies: 3
Views: 2,600
Posted By thomasvangurp
Hi MeganS, Do you have any references that...

Hi MeganS,

Do you have any references that indicate the source of this hexamer mispriming?

Forum: Bioinformatics 12-18-2011, 11:44 AM
Replies: 5
Views: 3,144
Posted By thomasvangurp
OLC vs de Bruijn Performance on heterogeneous 454-reads

Dear forum-members,

I've had a puzzling reply by a reviewer on the claim that:

"Differences in the accurary of assembly between heterogeneous 454- transcriptome reads between de bruijn and OLC...
Forum: Sample Prep / Library Generation 05-27-2011, 03:41 AM
Replies: 3
Views: 3,279
Posted By thomasvangurp
Question multiple rRNA peaks Biorad Experion

Dear All,

While testing my RNA samples for quality on the BioRad Experion i noticed multiple peaks before the 18S peak. The pattern is fairly consistent as shown in the image. Now, the software...
Forum: Literature Watch 11-18-2010, 12:52 AM
Replies: 1
Views: 2,884
Posted By thomasvangurp
Does anyone know if someone else has successfully...

Does anyone know if someone else has successfully applied this method? It sounds very promising for future whole genome sequencing efforts. Especially if one can multiplex the samples on the Hiseq
Forum: Illumina/Solexa 09-02-2010, 05:51 AM
Replies: 1
Views: 2,170
Posted By thomasvangurp
Illumina Assay Design Tool

Dear users,

Does anyone know which parameters the Illumina Assay Design tool uses to determine which sequences are used for SNP detection on the Golden gate or Infinium platform? Furthermore, is...
Forum: Bioinformatics 08-12-2010, 04:32 AM
Replies: 12
Views: 16,617
Posted By thomasvangurp
I would like to use Picard duplicate removal...

I would like to use Picard duplicate removal also. However, i ran into some trouble using a SAM-file outputted by CLC-Bio Genomics workbench. Anyone had an idead how to fix this issue?

Forum: Bioinformatics 08-13-2009, 10:34 AM
Replies: 0
Views: 1,820
Posted By thomasvangurp
Question Using AFLP to reduce template genome size

Dear Users,

I would like to ask your opinion about the following conceptual approach.

For comparison of methylation patterns in different individual plants (Taraxacum), we would like to assess...
Forum: Introductions 01-21-2009, 05:45 AM
Replies: 0
Views: 1,368
Posted By thomasvangurp
Smile Hello from Thomas

Hello there,
I'm new here. I'm studying Biology at Wageningen University. Currently I'm working on a new idea for improving methylation sensitive AFLP (MSAP) using the complete Arabidopsis...
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