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Forum: Service Providers 02-21-2011, 02:39 PM
Replies: 3
Views: 4,688
Posted By obig
The NGS-specific LIMS we are considering is...

The NGS-specific LIMS we are considering is miniLIMS from BioTeam. If anyone has experience with this system or any other NGS-specific LIMS we'd sure appreciate their experience. How long did it take...
Forum: Bioinformatics 01-27-2011, 02:43 PM
Replies: 14
Views: 7,357
Posted By obig
I'll add my two cents. Definitely go for...

I'll add my two cents. Definitely go for paired-end when doing RNAseq. Certain protocols (ChIP-seq, tag-seq) might make more sense with single-end data. But, RNAseq is definitely not one of them....
Forum: Bioinformatics 01-13-2011, 07:37 PM
Replies: 9
Views: 5,659
Posted By obig
Here is what Marioni et al (2008; Genome...

Here is what Marioni et al (2008; Genome Research. 18(9):1509-17 (http://genome.cshlp.org/content/18/9/1509.long)) have to say on the topic in their paper RNA-seq: an assessment of technical...
Forum: Bioinformatics 01-13-2011, 06:43 PM
Replies: 9
Views: 5,659
Posted By obig
RNA-seq technical replicates at library construction level

I apologize if this has been answered elsewhere but I can't find it. The forum and literature are full of analyzes that have looked at technical replicates in RNAseq where the same library is...
Forum: Bioinformatics 11-18-2010, 02:55 PM
Replies: 3
Views: 3,548
Posted By obig
I can see your confusion. There is something very...

I can see your confusion. There is something very strange about figure 1 in their paper. Panel (b) might make sense if what they were plotting was error rate relative to base position for a 40bp...
Forum: RNA Sequencing 11-17-2010, 07:34 PM
Replies: 23
Views: 9,787
Posted By obig
Oh. Sorry I see what you were saying now. This is...

Oh. Sorry I see what you were saying now. This is indeed the exact situation I have then. I found that rsyncing back and forth was sometimes pretty slow (many files). So, I found myself even...
Forum: RNA Sequencing 11-17-2010, 07:27 PM
Replies: 23
Views: 9,787
Posted By obig
I have the same issue with my data and analysis...

I have the same issue with my data and analysis servers not being mounted on the head nodes. I've found rsync useful for this. I was given a decent size data folder accessible by the cluster. I do...
Forum: RNA Sequencing 11-17-2010, 02:12 PM
Replies: 23
Views: 9,787
Posted By obig
Dear bioinfosm, I was responding to a...

Dear bioinfosm,

I was responding to a question from the user with user name = "micrornas". This thread doesn't actually have anything specifically to do with the biological entity called microRNA....
Forum: General 11-17-2010, 02:04 PM
Replies: 10
Views: 13,808
Posted By obig
If you prefer to use R/Bioconductor, you might...

If you prefer to use R/Bioconductor, you might investigate the BSgenome and Biostrings packages. Here's a document walking your through the process:...
Forum: RNA Sequencing 11-17-2010, 12:18 PM
Replies: 23
Views: 9,787
Posted By obig
alexa-seq cluster

I guess there are too many different cluster configurations for alexa-seq to anticipate. So, simple bash files are produced which can be run serially (for very small libraries) or submitted to your...
Forum: Introductions 11-17-2010, 11:04 AM
Replies: 373
Views: 135,858
Posted By obig
Hi all, I'm a postdoc at Lawrence Berkeley...

Hi all,

I'm a postdoc at Lawrence Berkeley National Laboratory. Before that I was at the Genome Sciences Centre in Vancouver. I've been working on RNAseq, ChIPseq, pathogen discovery and other...
Forum: RNA Sequencing 11-17-2010, 10:55 AM
Replies: 23
Views: 9,787
Posted By obig
single-end data

micrornas. I have processed single-end data with alexa-seq. I created dummy R2 qseq files with sequences of Ns at the same length as the real read and quality strings comprised of all "B" values....
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