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Forum: Sample Prep / Library Generation 01-15-2015, 01:12 AM
Replies: 68
Views: 23,004
Posted By EvilTwin
Hi Nighthawkrao, which metrics are of...

Hi Nighthawkrao,


which metrics are of predominant interest for you?


In terms of library complexity on whole transcriptome for 1 ng (rRNA-depleted) and below, CATS gives very good...
Forum: Sample Prep / Library Generation 11-12-2014, 04:54 AM
Replies: 68
Views: 23,004
Posted By EvilTwin
Hi sequencingfan, CATS can be...

Hi sequencingfan,



CATS can be directly used without additional preparations if your DNA is fragmented to ~ 150-200 bp after extraction, as is usual with plasma DNA.
It also works with...
Forum: Genomic Resequencing 07-06-2012, 01:55 AM
Replies: 9
Views: 5,925
Posted By EvilTwin
Hi sehrrot, Initially we also compared...

Hi sehrrot,

Initially we also compared Agilent50MB post-capture multiplexing and NimbleGen V3 pre-capture multiplexing on the same set of samples, and there were no dramatic differences concerning...
Forum: Genomic Resequencing 07-05-2012, 08:07 AM
Replies: 9
Views: 5,925
Posted By EvilTwin
Hi sehrrot, that is strange, we typically...

Hi sehrrot,

that is strange, we typically got 5-10 % (MarkDuplicates in Picard Tools). One run was exceptional with 25 % duplication, but as I understand there was some technical problem...
Forum: Genomic Resequencing 06-26-2012, 01:03 AM
Replies: 9
Views: 5,925
Posted By EvilTwin
@ Heisman, I just realized I never thanked...

@ Heisman,

I just realized I never thanked you for the hint on that paper, but still… thanks a lot!

As I understand, our sequencing core facility had at that time already applied the (or at...
Forum: Genomic Resequencing 06-26-2012, 12:53 AM
Replies: 9
Views: 5,925
Posted By EvilTwin
Hi sehrrot, how do you exactly calculate...

Hi sehrrot,

how do you exactly calculate your on-target and coverage data? Maybe I can learn something :-)

We tried the SeqCap EZ 3.0 and got ~ 70x average coverage per Exome when pooling 4...
Forum: Genomic Resequencing 01-31-2012, 05:26 AM
Replies: 9
Views: 5,925
Posted By EvilTwin
Pre-Capture Pooling with Nimblegen SeqCap EZ v3: SNP detection quality?

Dear all,

Does anyone have already some experience with the new Nimblegen SeqCap EZ v3 targeted Exome Enrichment kit, concerning pre-capture pooling?
The kit explicitly supports pre-capture...
Forum: Bioinformatics 11-01-2011, 11:34 AM
Replies: 22
Views: 6,140
Posted By EvilTwin
I once observed the same error when running bwa...

I once observed the same error when running bwa in a Virtual Box - Linux. No idea why. It should work if you use a non-virtual system.
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