Forum: General
07-26-2012, 05:23 PM
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Replies: 1
Views: 2,001
Agilent SureSelect Kit
Has anyone used Agilent SureSelect XT2 Kit? With regard to this kit, is it possible to pool more than 16 individuals on a single capture? Agilent says a max 16, but I am unsure if this is for some...
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Forum: Bioinformatics
07-12-2012, 01:44 PM
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Replies: 4
Views: 1,525
You might want to consider BUCKy:...
You might want to consider BUCKy: http://www.stat.wisc.edu/~ane/bucky/index.html. This program summarizes across individual gene trees to show the most common topology for the species tree.
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Forum: Bioinformatics
06-13-2012, 05:14 PM
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Replies: 2
Views: 1,871
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Forum: Bioinformatics
03-20-2012, 09:24 AM
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Replies: 7
Views: 4,896
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Forum: RNA Sequencing
03-20-2012, 09:22 AM
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Replies: 3
Views: 1,213
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Forum: Bioinformatics
02-21-2012, 06:03 PM
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Replies: 1
Views: 2,206
gene ontology
Hi all,
I am trying to do some pretty naive gene ontology profiling of my RNAseq data. These data are from a de novo assembly of a lizard genome. In the past, I had used Blast2Go, but I have found...
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Forum: Sample Prep / Library Generation
02-13-2012, 09:18 AM
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Replies: 23
Views: 52,862
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Forum: De novo discovery
02-10-2012, 11:13 AM
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Replies: 7
Views: 5,154
Hi LizBent,
I have been working on the exact...
Hi LizBent,
I have been working on the exact same problem and have come up with some metrics to estimate the quality of a transcriptome in the absence of a ref genome. Some stats that I have used...
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Forum: Sample Prep / Library Generation
02-08-2012, 02:19 PM
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Replies: 23
Views: 52,862
Hi there,
I got the exact same pattern you...
Hi there,
I got the exact same pattern you describe (couldn't see the image). See this post for what I found, what others suggested, and to see the end results. Let me know if you'd like more...
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Forum: Sample Prep / Library Generation
01-10-2012, 09:53 AM
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Replies: 17
Views: 11,344
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Forum: Bioinformatics
12-13-2011, 09:26 AM
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Replies: 5
Views: 2,932
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Forum: Bioinformatics
12-06-2011, 01:16 PM
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Replies: 15
Views: 6,195
I think I found a small hiccup in Trimmomatic...
I think I found a small hiccup in Trimmomatic (easily fixed by the user, but it might be good to clarify somewhere on the website) -- when providing sequences for the adapters, the file has to be in...
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Forum: Sample Prep / Library Generation
11-14-2011, 05:48 PM
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Replies: 17
Views: 11,344
So, I ended up size-selecting my libraries, and...
So, I ended up size-selecting my libraries, and then I used Bioanalyzer to look at the curve -- and it was exactly the same. Again, the desired peak at 300 bp and the higher MW peak centered around...
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Forum: Sample Prep / Library Generation
11-09-2011, 04:55 PM
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Replies: 17
Views: 11,344
This is TAE EtBr and I did 15 cycles of...
This is TAE EtBr and I did 15 cycles of enrichment PCR.
Not sure what this is, but I went ahead and size selected. I'll let you all know when I get my data...hopefully this is just a weird...
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Forum: Sample Prep / Library Generation
11-08-2011, 06:01 PM
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Replies: 17
Views: 11,344
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Forum: Sample Prep / Library Generation
11-08-2011, 12:14 PM
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Replies: 17
Views: 11,344
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Forum: Sample Prep / Library Generation
11-07-2011, 05:54 PM
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Replies: 17
Views: 11,344
When I contacted Illumina, they gave me three...
When I contacted Illumina, they gave me three possible explanations:
1. Incomplete fragmentation (which seems unlikely, given that I was using RNA within the range of what the recommended and a long...
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Forum: Sample Prep / Library Generation
11-02-2011, 05:18 PM
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Replies: 17
Views: 11,344
double peak in mRNA truseq kit
Hi all,
I have been doing some mRNA TruSeq sample prep, using the protocol *exactly* as advised by the Illumina folk (using PolyT beads to get mRNA, fragmenting for 7 minutes chemically, 15 PCR...
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Forum: Sample Prep / Library Generation
10-25-2011, 10:06 AM
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Replies: 22
Views: 9,371
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Forum: Bioinformatics
01-09-2009, 01:57 PM
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Replies: 7
Views: 4,474
Alignment Questions
Dear all,
I am working with 454 sequence from a transcriptome of an organism 2 million years diverged from the rat. De novo assembly using Newbler was very disappointing, so we are trying other...
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