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Forum: Illumina/Solexa 04-22-2015, 02:45 PM
Replies: 14
Views: 4,031
Posted By nbogard
What if the number of cycles is longer than the...

What if the number of cycles is longer than the insert + adapter + flow cell oligo?
Forum: Illumina/Solexa 09-05-2012, 07:09 AM
Replies: 37
Views: 42,042
Posted By nbogard
Can you please elaborate on this? I am having...

Can you please elaborate on this? I am having similar problems with cluster generation on MiSeq but expect that my new libraries with PE adapters will work fine. My concern is whether or not the...
Forum: Sample Prep / Library Generation 07-02-2012, 10:32 PM
Replies: 4
Views: 3,295
Posted By nbogard
Thank you so much for sharing this, Phillip. Just...

Thank you so much for sharing this, Phillip. Just the info I had been looking for.

Do you know, or could reason, whether a phosphorothioate linkage between the last two 3' bases (near the nick...
Forum: General 02-13-2012, 10:19 PM
Replies: 3
Views: 6,306
Posted By nbogard
Contig length, k-mer coverage, and differential expression

I'm working with some data where I have a read count and k-mer coverage (Ck) for a set of contigs and scaffolds across different conditions. I've recently heard and read a few very confusing...
Forum: SOLiD 12-01-2011, 06:19 PM
Replies: 2
Views: 2,576
Posted By nbogard
Thanks much, Phillip! I found the patent...

Thanks much, Phillip!

I found the patent info you referred too, it helps a lot. Looks like I am going to have to do a lot of optimization if I go the custom route.

Very interesting about the...
Forum: SOLiD 11-30-2011, 11:20 PM
Replies: 2
Views: 2,576
Posted By nbogard
Custom SOLID Adapters for RNA-Seq

Has anyone here designed custom, SOLID-like adapters for preparing RNA-Seq libraries? Specifically, I'd like to use forward (F) and reverse (R), splint-like adapters (with poly-N overhangs) that...
Forum: Illumina/Solexa 07-07-2011, 08:33 PM
Replies: 145
Views: 318,044
Posted By nbogard
Hi, frc1230! Your schematic is great. Thanks for...

Hi, frc1230! Your schematic is great. Thanks for the contribution.

-Nick
Forum: Illumina/Solexa 06-27-2011, 04:28 PM
Replies: 145
Views: 318,044
Posted By nbogard
Thanks again, sci_guy. Makes sense. All the...

Thanks again, sci_guy. Makes sense.

All the best!
Forum: Illumina/Solexa 06-27-2011, 01:44 AM
Replies: 145
Views: 318,044
Posted By nbogard
Thanks sci_guy! Is the exonuclease activity...

Thanks sci_guy!

Is the exonuclease activity in the ligation prep from leftover T4 DNA Pol used in the earlier end-repair reaction? If the contamination is significant, that would explain the...
Forum: Illumina/Solexa 06-27-2011, 12:36 AM
Replies: 145
Views: 318,044
Posted By nbogard
Why is the phosphorothioate modification (in the...

Why is the phosphorothioate modification (in the adapter) at the 3'-end that is proximal to the ligation? Shouldn't that 3'-end be protected after the ligation? I don't understand why the...
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