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Forum: Illumina/Solexa 09-27-2011, 08:24 AM
Replies: 7
Views: 3,262
Posted By NearyJL78
I really wish I'd asked this question here...

I really wish I'd asked this question here sooner! THANK YOU for the info about the TruSeq adapters being methylated!
Forum: Illumina/Solexa 09-27-2011, 08:19 AM
Replies: 7
Views: 3,262
Posted By NearyJL78
I'm not sure if they are quanititating with qPCR...

I'm not sure if they are quanititating with qPCR but I am forwarding all of this to my boss. I just wanted to thank you personally for the links to your blog, which are exceedingly helpful.
Forum: Illumina/Solexa 09-27-2011, 07:54 AM
Replies: 7
Views: 3,262
Posted By NearyJL78
Thanks Simon. Since you've run these types of...

Thanks Simon. Since you've run these types of experiments I have one more question for you. Overall do you find a much increased GC% in the NGS data after immunoprecip in comparison to control?
...
Forum: Illumina/Solexa 09-27-2011, 07:43 AM
Replies: 7
Views: 3,262
Posted By NearyJL78
Wow thank you all so much for your assistance,...

Wow thank you all so much for your assistance, especially about the TruSeq adapters being methylated!
Forum: Illumina/Solexa 09-26-2011, 01:26 PM
Replies: 7
Views: 3,262
Posted By NearyJL78
Me-DIP-seq troubleshooting, several questions

Hi all,

We are in the process of optimizing our Me-Dip-seq protocol using TruSeq multiplexing on the Illumina HiSeq2000 and we have been puzzled by (or cursed with) a variety of problems.

I...
Forum: Bioinformatics 05-16-2011, 11:08 AM
Replies: 2
Views: 5,837
Posted By NearyJL78
Thanks steven!

Thanks steven!
Forum: Bioinformatics 05-11-2011, 12:20 PM
Replies: 2
Views: 5,837
Posted By NearyJL78
Promoter regions hg19

Does anyone know of a downloadable data set that lists all of the predicted promoter regions in the human genome? I understand promoters can be defined in different ways, but that is unimportant as...
Forum: Bioinformatics 05-09-2011, 12:28 PM
Replies: 3
Views: 2,712
Posted By NearyJL78
Also, its the second number (.93-.96 in your...

Also, its the second number (.93-.96 in your case) that you might be looking at. That represents the reproducibility of the experiment with you current conditions... if you look at the graph you can...
Forum: Bioinformatics 05-09-2011, 11:26 AM
Replies: 3
Views: 2,712
Posted By NearyJL78
EDIT - the paragraph below is referring to the...

EDIT - the paragraph below is referring to the next steps in MEDIPS analysis, sorry! I'm typing the answer to your question (AS I UNDERSTAND IT) after the ***


I am just starting with MEDIPS...
Forum: Bioinformatics 05-06-2011, 10:58 AM
Replies: 5
Views: 3,520
Posted By NearyJL78
Bedtools was definitely the easiest. I'm going to...

Bedtools was definitely the easiest. I'm going to stick with that, thanks everyone!
Forum: Bioinformatics 05-05-2011, 11:01 AM
Replies: 5
Views: 3,520
Posted By NearyJL78
Thank you for your help! Both suggestions make...

Thank you for your help! Both suggestions make sense and while I haven't used bedfiles I think maybe I will give it a try :-)
Forum: Bioinformatics 05-02-2011, 12:15 PM
Replies: 5
Views: 3,520
Posted By NearyJL78
Query bam files, awk question

Hello,

I am trying to generate four column files for methylation analysis from my NGS alignments against the human genome (single and paired-end). The file needs to contain the following...
Forum: Illumina/Solexa 02-16-2011, 10:39 AM
Replies: 8
Views: 4,846
Posted By NearyJL78
We've used an approach similar to the Craig...

We've used an approach similar to the Craig paper, with our own 28 adapters. It worked very well, but now we are trying to Illumina multiplexing kits to speed up sample prep. This is not going as...
Forum: Bioinformatics 02-16-2011, 10:17 AM
Replies: 1
Views: 4,855
Posted By NearyJL78
Are you using your own barcodes or the Illumina...

Are you using your own barcodes or the Illumina multiplexing kit? The most recent version of NextGENe handles the demultiplexing of the data from the kits. I'm also trying to get it to work with CLC...
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