Forum: Bioinformatics
06-28-2013, 12:20 PM
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Replies: 6
Views: 1,870
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Forum: Bioinformatics
04-05-2012, 10:46 AM
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Replies: 16
Views: 7,287
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Forum: Illumina/Solexa
12-13-2010, 10:36 AM
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Replies: 17
Views: 7,076
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Forum: Helicos / Direct Genomics
11-30-2010, 01:44 PM
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Replies: 18
Views: 14,314
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Forum: Helicos / Direct Genomics
11-22-2010, 12:08 PM
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Replies: 18
Views: 14,314
They got delisted because their stock price...
They got delisted because their stock price didn't have a price level over $1 per NASDAQ rules.
I have experience with Helicos mRNA-Seq (having just submitted a paper using the technology).
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Forum: Illumina/Solexa
11-22-2010, 09:07 AM
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Replies: 9
Views: 4,952
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Forum: RNA Sequencing
11-17-2010, 08:30 PM
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Replies: 23
Views: 10,143
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Forum: RNA Sequencing
11-17-2010, 08:18 PM
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Replies: 23
Views: 10,143
Thanks for the replies. It sounds like the...
Thanks for the replies. It sounds like the Lawrencium is set up almost exactly like our flux cluster here at UMich. The only issue that we have is that our head nodes don't have our data drives...
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Forum: RNA Sequencing
11-17-2010, 12:00 PM
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Replies: 23
Views: 10,143
We're trying to get the heavy lifting...
We're trying to get the heavy lifting (preprocessing, alignment) parts of ALEXA going on our cluster which uses the Torque scheduler. I know that ALEXA was designed to run on a cluster, was there a...
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Forum: Illumina/Solexa
11-08-2010, 08:02 AM
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Replies: 9
Views: 4,952
HiSeq 2000 RNA-Seq Mapping Rates
We're running and mapping human samples on our new(ish) HiSeq2000 and we're seeing some low mapping rates out of ELAND. Even if you don't run ELAND, I'd be interested in hearing what other HiSeq...
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Forum: Bioinformatics
10-25-2010, 12:51 PM
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Replies: 30
Views: 10,599
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Forum: RNA Sequencing
10-19-2010, 01:47 PM
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Replies: 29
Views: 13,448
I have a few dozen lanes to run (PE 2x50 GA2...
I have a few dozen lanes to run (PE 2x50 GA2 runs). I suppose I can set it up to run on a cluster I have access to. My experiences have mostly been with SAW (published by some people I know),...
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Forum: RNA Sequencing
10-19-2010, 01:23 PM
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Replies: 29
Views: 13,448
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Forum: RNA Sequencing
10-14-2010, 08:24 PM
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Replies: 23
Views: 10,143
I figured out my issue. Now I have another...
I figured out my issue. Now I have another question: have you processed any HiSeq data with the pipeline? I started a couple HiSeq lanes 4 hours ago and it isn't even done with the read...
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Forum: RNA Sequencing
10-14-2010, 09:36 AM
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Replies: 23
Views: 10,143
I'm playing with the ALEXA-Seq image, and I'm...
I'm playing with the ALEXA-Seq image, and I'm wondering what kind of data path the scripts require. I ask because I just point it at a common folder /home/alexa-seq/seq_files with .fastq files named...
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Forum: Bioinformatics
09-27-2010, 08:51 AM
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Replies: 4
Views: 3,052
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Forum: Illumina/Solexa
09-27-2010, 08:47 AM
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Replies: 17
Views: 7,076
We've seen a similarly huge increase in the...
We've seen a similarly huge increase in the processing times. My personal experience: aligning ~180-200 million 2x100PE whole-genome low coverage data reads from single lanes with BWA from...
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Forum: General
09-27-2010, 08:42 AM
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Replies: 2
Views: 2,107
Hi Joanne. How about trying to align to both...
Hi Joanne. How about trying to align to both exons and splice junctions using short seeds and fairly tight thresholds (20mer, 1 mismatch)? You might end up with some reads that align as both small...
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Forum: Bioinformatics
09-22-2010, 01:38 PM
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Replies: 5
Views: 6,134
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Forum: Bioinformatics
09-03-2010, 09:57 AM
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Replies: 13
Views: 16,430
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Forum: Literature Watch
08-30-2010, 03:05 PM
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Replies: 0
Views: 3,468
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Forum: Bioinformatics
08-27-2010, 02:37 PM
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Replies: 40
Views: 16,022
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Forum: De novo discovery
08-27-2010, 02:03 PM
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Replies: 7
Views: 9,417
Here's a page with the link for the DSN...
Here's a page with the link for the DSN normalization protocol. I can't comment further because I honestly don't remember the specifics.
http://www.illumina.com/applications/sequencing/rna.ilmn
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Forum: Bioinformatics
08-27-2010, 01:58 PM
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Replies: 8
Views: 3,797
There is also the consideration that (to my...
There is also the consideration that (to my admittedly shallow understanding) TopHat only uses the set of canonical splice signal sequences. Unfortunately, I can't recommend anything better - I was...
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Forum: Bioinformatics
08-27-2010, 01:56 PM
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Replies: 40
Views: 16,022
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