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Forum: Sample Prep / Library Generation 03-30-2017, 07:27 AM
Replies: 4
Views: 4,082
Posted By IanAWarren
Thank you very much for the responses. I will...

Thank you very much for the responses. I will give these protocols a go and see what happens.

Fingers crossed (when not pipetting!)
Forum: Sample Prep / Library Generation 03-29-2017, 05:54 AM
Replies: 4
Views: 4,082
Posted By IanAWarren
High Molecular Weight genomic DNA extraction

Hello,

Our lab is looking into doing some high molecular weight DNA extractions for use with the latest nanopore sequencing instruments.

Does anyone have any recommendations for the best...
Forum: Sample Prep / Library Generation 11-17-2016, 12:15 AM
Replies: 4
Views: 2,019
Posted By IanAWarren
Hello, Thank you for your answers. ...

Hello,

Thank you for your answers.

What conditions did you use for your Covaris machine? We have not got close to the sizes we want (actually too small now) and we are fine tuning. We have...
Forum: Sample Prep / Library Generation 11-16-2016, 05:14 AM
Replies: 4
Views: 2,019
Posted By IanAWarren
Shearing digested DNA for RADseq

Hello,

I am making libraries for RADseq. I am trying out the Covaris ME220 for shearing the digested DNA. The shearing seems to be highly inefficient compared to what is given in the protocol book...
Forum: Illumina/Solexa 05-14-2015, 02:57 AM
Replies: 0
Views: 1,156
Posted By IanAWarren
Designing primers on assembly: bizarre problem

This is a bizarre problem that happened a couple of years ago to myself and is now happening to a colleague.

The aim is to design primers for PCR using a de novo transcriptome assembly. However,...
Forum: Bioinformatics 01-07-2015, 11:43 PM
Replies: 1
Views: 1,639
Posted By IanAWarren
To answer my own question, the NCBI said this: ...

To answer my own question, the NCBI said this:

When you run blastn, you are by default running megablast, which has a
default word size of 28. To run blastn with word size 11, add this option:
...
Forum: Bioinformatics 01-07-2015, 05:49 AM
Replies: 1
Views: 1,639
Posted By IanAWarren
blastn default settings

Hello,

I am running blastn locally using BLASTN 2.2.29+ (and have also tried BLASTN 2.2.24+)

According to the manual, the default word size for a blastn search is 11. However, if I set the word...
Forum: Bioinformatics 01-02-2015, 07:25 AM
Replies: 3
Views: 2,368
Posted By IanAWarren
Thank you for the help! I need mdust as part of...

Thank you for the help! I need mdust as part of another package (MITE Hunter). I will try both methods and see which works.
Forum: Bioinformatics 01-02-2015, 01:31 AM
Replies: 3
Views: 2,368
Posted By IanAWarren
Downloading mDUST

Hello,

I am searching for the program mDUST. It used to be available on the TGI website, but that is currently unavailable

http://compbio.dfci.harvard.edu/tgi/

Thank you in advance for any...
Forum: 454 Pyrosequencing 02-20-2013, 05:48 AM
Replies: 14
Views: 14,689
Posted By IanAWarren
We also installed version 2.8 on BioLinux 6 using...

We also installed version 2.8 on BioLinux 6 using the above information.

Thank you for the post!
Forum: Bioinformatics 02-06-2013, 03:15 AM
Replies: 1
Views: 1,184
Posted By IanAWarren
Problem with a CLC 454 transcriptome assembly

Hello,

We are working on a 454 de novo assembly of transcriptome data using CLC's de Bruijn graphs method.

We are encountering two major problems when we look at the assembly and were hoping...
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