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Forum: Introductions 05-08-2013, 09:44 PM
Replies: 14
Views: 11,435
Posted By obscurite
geyihe, I'm associated with a lab that's working...

geyihe, I'm associated with a lab that's working on Borrelia -- please get in touch if you get a chance. :)
Forum: RNA Sequencing 05-02-2013, 10:39 AM
Replies: 10
Views: 10,637
Posted By obscurite
Thanks for the tool and strategy suggestions. We...

Thanks for the tool and strategy suggestions. We have found some rRNA (despite depletion) and are running the QC tools. We are aware of ribopicker. Does anyone have a favorite technique for cleaning...
Forum: RNA Sequencing 04-30-2013, 07:35 AM
Replies: 10
Views: 10,637
Posted By obscurite
Hi Alex. Thanks for weighing in. Here's one...

Hi Alex. Thanks for weighing in. Here's one particularly low mapping count.

Started job on | Mar 15 04:59:21
Started mapping on | Mar...
Forum: RNA Sequencing 04-29-2013, 08:46 PM
Replies: 10
Views: 10,637
Posted By obscurite
Typical alignment mapping percentage with genome?

What are typical mapping percentages for alignment? My samples are giving me an average of approx. 25% mapping coverage (from pair end 100bp reads). STAR produces somewhat fewer mappings than Tophat,...
Forum: General 03-01-2013, 07:07 PM
Replies: 2
Views: 1,068
Posted By obscurite
Thanks GenoMax. It so happens that's the paper...

Thanks GenoMax. It so happens that's the paper and protocol we started with, so I've considered using the iGenome fly data, but the problem is the genome is still hefty as are the data files. I think...
Forum: General 02-27-2013, 08:27 PM
Replies: 2
Views: 1,068
Posted By obscurite
Minimal RNA seq dataset for performance eval

Hello all. I'd like to compare the speed for the tophat/cuffdiff protocol on various hardware platforms to see which is the speediest combination. Is there a small genome/sample set that anyone knows...
Forum: Introductions 02-27-2013, 06:20 PM
Replies: 0
Views: 974
Posted By obscurite
Hello from Hunter College in NYC!

In my former life I was a software engineer and IT guy. I'm finishing a BA in bioinformatics at Hunter College and I'm interested in molecular level engineering and bioinformatics.

I'm working on...
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