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Forum: General 07-26-2012, 05:23 PM
Replies: 1
Views: 2,001
Posted By ssing
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...
Forum: Bioinformatics 07-12-2012, 01:44 PM
Replies: 4
Views: 1,525
Posted By ssing
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.
Forum: Bioinformatics 06-13-2012, 05:14 PM
Replies: 2
Views: 1,871
Posted By ssing
It doesn't look like you did anything wrong. I...

It doesn't look like you did anything wrong. I had similar results; while OASES gives very accurately assembled contigs, it gives many fewer contigs of much shorter length.
Forum: Bioinformatics 03-20-2012, 09:24 AM
Replies: 7
Views: 4,896
Posted By ssing
I also think the 'ape' package in R is great for...

I also think the 'ape' package in R is great for making attractive trees, though it does require knowing R.
Forum: RNA Sequencing 03-20-2012, 09:22 AM
Replies: 3
Views: 1,213
Posted By ssing
I have tried mapping to a genome from an organism...

I have tried mapping to a genome from an organism about 15-20 mya from the organism of interest. I found that I only had a slight decrease in mapping efficiency (90 -> 80%) but that more divergent...
Forum: Bioinformatics 02-21-2012, 06:03 PM
Replies: 1
Views: 2,206
Posted By ssing
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...
Forum: Sample Prep / Library Generation 02-13-2012, 09:18 AM
Replies: 23
Views: 52,862
Posted By ssing
Hi Phillip, It was a pre-stained agarose...

Hi Phillip,

It was a pre-stained agarose gel. Thanks!

Sonal
Forum: De novo discovery 02-10-2012, 11:13 AM
Replies: 7
Views: 5,154
Posted By ssing
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...
Forum: Sample Prep / Library Generation 02-08-2012, 02:19 PM
Replies: 23
Views: 52,862
Posted By ssing
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...
Forum: Sample Prep / Library Generation 01-10-2012, 09:53 AM
Replies: 17
Views: 11,344
Posted By ssing
Just wanted to follow up and say that I got good...

Just wanted to follow up and say that I got good quality sequences at good yields on the HiSeq. Our sequencing facility head said he had seen similar bioanalyzer profiles with the TruSeq kit -- why...
Forum: Bioinformatics 12-13-2011, 09:26 AM
Replies: 5
Views: 2,932
Posted By ssing
RAxML should be able to handle that many tips,...

RAxML should be able to handle that many tips, but it cannot align... GARLI is also efficient at making large trees from alignments, but I don't know what its upper limit is.
Forum: Bioinformatics 12-06-2011, 01:16 PM
Replies: 15
Views: 6,195
Posted By ssing
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...
Forum: Sample Prep / Library Generation 11-14-2011, 05:48 PM
Replies: 17
Views: 11,344
Posted By ssing
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...
Forum: Sample Prep / Library Generation 11-09-2011, 04:55 PM
Replies: 17
Views: 11,344
Posted By ssing
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...
Forum: Sample Prep / Library Generation 11-08-2011, 06:01 PM
Replies: 17
Views: 11,344
Posted By ssing
Hi Philip, See attached. The ladder is a 100...

Hi Philip,

See attached. The ladder is a 100 bp ladder (NEB).
Forum: Sample Prep / Library Generation 11-08-2011, 12:14 PM
Replies: 17
Views: 11,344
Posted By ssing
In fact, this does not appear to be due to beads....

In fact, this does not appear to be due to beads. I am not sure what the peak is, but I am going to size select ... trivial exercise and worth ensuring good cluster generation.
Forum: Sample Prep / Library Generation 11-07-2011, 05:54 PM
Replies: 17
Views: 11,344
Posted By ssing
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...
Forum: Sample Prep / Library Generation 11-02-2011, 05:18 PM
Replies: 17
Views: 11,344
Posted By ssing
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...
Forum: Sample Prep / Library Generation 10-25-2011, 10:06 AM
Replies: 22
Views: 9,371
Posted By ssing
I had horrible experience with the Nextflex kits,...

I had horrible experience with the Nextflex kits, but using the same starting material with the TruSeq kits, I got excellent results. I am not sure if this is just me...

Bioo Scientific staff was...
Forum: Bioinformatics 01-09-2009, 01:57 PM
Replies: 7
Views: 4,474
Posted By ssing
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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