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Forum: Illumina/Solexa 11-17-2011, 02:00 PM
Replies: 38
Views: 19,007
Posted By Simcom
OK, that is good to hear. I'm not sure why my...

OK, that is good to hear. I'm not sure why my core was having trouble spiking 1:1 gDNA.
Forum: Illumina/Solexa 11-17-2011, 01:52 PM
Replies: 38
Views: 19,007
Posted By Simcom
Yep, I planned on including both primers. Thank...

Yep, I planned on including both primers. Thank you so much for your help, I really appreciate it. :D
Forum: Illumina/Solexa 11-17-2011, 01:11 PM
Replies: 38
Views: 19,007
Posted By Simcom
Thanks, this gives me confidence. Just to be...

Thanks, this gives me confidence. Just to be sure though: do the adapter-adapter ligation reads come back in the data, or does the machine throw them out and not include them in sequencing results? ...
Forum: Illumina/Solexa 11-17-2011, 01:04 PM
Replies: 38
Views: 19,007
Posted By Simcom
Yep, exactly. Sadly my boss insisted on having a...

Yep, exactly. Sadly my boss insisted on having a library that we can do single read OR paired end on (a money saving move potentially), so I had to design the junction on the first read side. And...
Forum: Illumina/Solexa 11-17-2011, 12:59 PM
Replies: 38
Views: 19,007
Posted By Simcom
I agree with you that hybridization is unlikely,...

I agree with you that hybridization is unlikely, but if it does happen it will be indistinguishable from an actual integration. Among other things, we are interested in mapping low-abundance...
Forum: Illumina/Solexa 11-17-2011, 12:50 PM
Replies: 38
Views: 19,007
Posted By Simcom
I think you are misunderstanding the problem. ...

I think you are misunderstanding the problem. The issue is, because the first 5nt of read #1 are going to be all identical among clusters, and the machine uses these 5nt to call clusters, the...
Forum: Illumina/Solexa 11-17-2011, 12:19 PM
Replies: 38
Views: 19,007
Posted By Simcom
I am sequencing viral DNA/gDNA integration...

I am sequencing viral DNA/gDNA integration junctions, so I am using that 5 nucleotides of viral DNA as a type of 'verification', that indeed a read contains the junction between viral DNA and gDNA,...
Forum: Illumina/Solexa 11-17-2011, 11:23 AM
Replies: 38
Views: 19,007
Posted By Simcom
Sequencing a Low diversity library on the HiSeq

I am preparing a custom multiplexed library that will fall into the "low diversity" category. Low diversity meaning the first 5 nucleotides of read 1 will be identical among all clusters. There is...
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