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Forum: Bioinformatics 08-04-2014, 07:14 AM
Replies: 0
Views: 1,143
Posted By BAJ
Predicting promoter sites from NGS experiments

Hi,

is it possible to predict promoter sites from NGS experiments? Given a set of RNAseq experiments (human, triplicates) of several biological conditions (3) can I predict a regulation network...
Forum: Bioinformatics 04-14-2011, 04:56 AM
Replies: 3
Views: 2,681
Posted By BAJ
One example on the memory: I am currently...

One example on the memory:
I am currently running 6 nodes for reading BAM files in parallel, each table consists of some 300 M rows. The memory footprint is about 5 GB though I allocated 16 GB on a...
Forum: Bioinformatics 04-13-2011, 09:44 PM
Replies: 3
Views: 2,681
Posted By BAJ
I am using it for production in our NGS service...

I am using it for production in our NGS service facility. We are mainly concerned with anything but resequencing and SNPs.
It is very good for prototyping and then moving to production for tasks...
Forum: Bioinformatics 04-12-2011, 06:53 AM
Replies: 3
Views: 2,681
Posted By BAJ
Smile NGS functionality for KNIME

Hi,

I am very excited that I can share now with you my nodes and workflows that I created for NGS data analysis in KNIME.

KNIME is a workflow management system. Some of its features include:
...
Forum: RNA Sequencing 03-25-2011, 12:18 PM
Replies: 1
Views: 1,435
Posted By BAJ
Problem solved, the file wasn't installed... Thx

Problem solved, the file wasn't installed...
Thx
Forum: RNA Sequencing 03-25-2011, 11:18 AM
Replies: 1
Views: 1,435
Posted By BAJ
Unhappy hmmSplicer problem with initialHMM.txt

Hi,

I am trying to run hmmSplicer and I get the following error message:
IOError: [Errno 2] No such file or directory: 'initialHMM.txt'

Does anyone know what this means?

I haven't...
Forum: Academic/Non-Profit Jobs 01-19-2011, 10:36 PM
Replies: 0
Views: 3,239
Posted By BAJ
Post-doctoral position (Paris, France)

Post-doctoral position in bioinformatics: next-generation sequencing (NGS) analysis for the study of host-viral interaction in dengue infection, Institut Pasteur, Paris, FRANCE.

The objective is...
Forum: Bioinformatics 01-17-2011, 04:34 AM
Replies: 8
Views: 3,796
Posted By BAJ
Hi, I would be interested in how you actually...

Hi,
I would be interested in how you actually compared the different algorithms?
You say you used an existing data set... Why don't you use a constructed one? and how do you know what is true or...
Forum: Bioinformatics 08-26-2009, 04:57 AM
Replies: 48
Views: 20,520
Posted By BAJ
sequence identifiers like >chrY_random

retracting comment. I have to check some more on my side first.
Sorry,
Bernd
Forum: Bioinformatics 04-16-2009, 05:50 AM
Replies: 13
Views: 16,610
Posted By BAJ
maybe you can also describe the various header...

maybe you can also describe the various header lines and what they mean...
Illumina gives something like this:
@HWI-EAS285:1:1:1582:1499#0/1
swift outputs:
@L1-100:474:2

Unfortunately I don't...
Forum: Bioinformatics 04-15-2009, 05:47 AM
Replies: 0
Views: 1,695
Posted By BAJ
swift related question

Hi,

I am working on NGS/Solexa data analysis. I am currently experimenting with swift for the image analysis, having some very encouraging results.

I am looking for a way to view/extract the...
Forum: Bioinformatics 02-24-2009, 12:25 AM
Replies: 2
Views: 1,904
Posted By BAJ
I just heard back from techsupport at illumina...

I just heard back from techsupport at illumina that this is a property of pipeline 1.0 whereas pipeline 1.3.2 is independent of the alignment.
Forum: Bioinformatics 02-23-2009, 02:17 AM
Replies: 24
Views: 20,314
Posted By BAJ
conversion table for solexa and Phred

I found this table useful it contains both scores for solexa and phred...

http://www.genographia.org/portal/topics/reports/qualitysheet.pdf/at_download/file

It is in PDF fromat...
Forum: Bioinformatics 02-23-2009, 01:12 AM
Replies: 2
Views: 1,904
Posted By BAJ
comparing results from two different reference genomes

we have a Solexa experiment that seems to be contaminated with a different genome than the one we were originally aiming at. The genomes have very different sizes (mouse vs. pombe) and if I...
Forum: Introductions 02-22-2009, 11:23 PM
Replies: 0
Views: 1,368
Posted By BAJ
New @ the Pasteur Institute new to NGS

Hi,
my name is Bernd and I am just in the process of moving from New York (what a wonderful city) to Paris (I haven't quite yet made up my mind on which one is more wonderful a city). I started...
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