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Forum: RNA Sequencing 10-14-2011, 07:25 AM
Replies: 2
Views: 4,788
Posted By Inti
RNA-seq poly-A vs ribo minus

Hi guys,
I have been doing some RNA-seq experiments with polyA selected and ribo minus. Unfortunately after estimation of gene expression using cufflinks, cuffcompare etc., the overlap between the 2...
Forum: RNA Sequencing 10-12-2011, 03:11 AM
Replies: 0
Views: 1,329
Posted By Inti
Strand orientation after tophat mapping

Hi guys,
I'm doing a strand specific RNA-seq with dUTP incorporation during the second strand synthesis of cDNA and posterior UDgase treatment. after the mapping of the reads using tophat I get the...
Forum: Academic/Non-Profit Jobs 05-12-2011, 03:55 AM
Replies: 0
Views: 1,696
Posted By Inti
Research Assistant-Max Planck Institute Freiburg

The Max Planck Institute of Immunobiology and Epigenetics in Freiburg, Germany, invites applications for the position of a:
Research Assistant
to support our deep-sequencing facility and a...
Forum: Bioinformatics 03-18-2011, 02:58 AM
Replies: 0
Views: 987
Posted By Inti
CUFF_id -> Gene symbol tool?

Hi guys,
I have seen that this topic has been discussed previously but so far the answers are not so clear.
Does somebody has a list of equivalents between CUFF_id's and gene symbols???
Is there...
Forum: Epigenetics 01-17-2011, 07:35 AM
Replies: 5
Views: 5,950
Posted By Inti
I usually block the magnetic A or G beads only...

I usually block the magnetic A or G beads only with BSA for 2 hours and bind the antibody first rather than put the AB in the sample and then the magnetic beads and the ChIPs looks very clean
Forum: RNA Sequencing 01-17-2011, 06:46 AM
Replies: 0
Views: 1,868
Posted By Inti
RNA-seq for differential expression

Hello!
We would like to start some RNA-seq experiments for quantitation and differential expression but I am not sure how deep should we sequence a sample to have enough coverage and have a good...
Forum: Bioinformatics 11-17-2010, 03:55 AM
Replies: 2
Views: 1,770
Posted By Inti
which alignment tool allows to anchor pair end reads over repeats?

Hi guys,
I'm having a problem using Eland for pair end alignment over repeats since it seem to need both reads to be unique to match the pair.
Is there any option to specify that it should use the...
Forum: Bioinformatics 08-13-2009, 08:02 AM
Replies: 3
Views: 1,417
Posted By Inti
Hey Nix! Thanks for the reply, I'm now...

Hey Nix!

Thanks for the reply, I'm now taking the tutorial and is great until now!
Forum: Bioinformatics 08-11-2009, 03:10 AM
Replies: 3
Views: 1,417
Posted By Inti
Bioinformatics for Biologists?

Hello guys!
Can any of you suggest some basic readings on how to start to learn basic bioinformatics to work with solexa data. I'm biologist and my bioinformatics knowledge is cero :( and I want to...
Forum: Epigenetics 03-30-2009, 02:14 AM
Replies: 14
Views: 5,992
Posted By Inti
No enrichment in ChIP-seq

Hi guys,
I'm doing some ChIP-seq for k4me3 and k27me3 using the GAII (illumina) and although I see a clear difference in my control PCR (comparing on and off genes) I can not see any difference...
Forum: Academic/Non-Profit Jobs 02-04-2009, 06:29 AM
Replies: 0
Views: 1,944
Posted By Inti
2 Bioinformaticians wanted

Hi guys, we are looking for 2 bioinformaticians for a new Next Gen Seq department at the Max Plank Institute for immunbiology in Freiburg Germany.
The complete info is in:...
Forum: Bioinformatics 07-08-2008, 02:44 AM
Replies: 236
Views: 529,699
Posted By Inti
Does any of you guys have tryed the Genomatix...

Does any of you guys have tryed the Genomatix products for Next Gen Seq?
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