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Forum: Bioinformatics 03-14-2016, 04:42 AM
Replies: 1
Views: 1,670
Posted By simon_seq
Fisher's exact test in RNA-Seq

In RNA-Seq analysis it is common to use tests analogous to Fisher's exact test to evaluate whether a gene is differentially expressed in two measured conditions.

Fisher's exact test relies on...
Forum: Bioinformatics 02-02-2016, 08:42 AM
Replies: 0
Views: 1,303
Posted By simon_seq
Automated primer walking

Hi all,
I'm trying to generate a list of oligonucleotide primers for Sanger sequencing, such that for an arbitrarily large DNA sequence I would get an optimised oligonucleotide every ca. 500 bases....
Forum: Bioinformatics 08-27-2015, 10:59 AM
Replies: 4
Views: 2,244
Posted By simon_seq
And to extend my question, would I be fine to...

And to extend my question, would I be fine to apply a LOESS transformation? It appears to me that in some of my conditions, there are very active targets, which then cause a bias in reads. Thus, a...
Forum: Bioinformatics 08-27-2015, 10:54 AM
Replies: 4
Views: 2,244
Posted By simon_seq
Thanks a lot for your quick answer! May I...

Thanks a lot for your quick answer!

May I ask, what are the formal constraints when changing normalization methods, such that the basic concept of DESeq(2) still works? Ie. assumption of a...
Forum: Bioinformatics 08-27-2015, 07:24 AM
Replies: 4
Views: 2,244
Posted By simon_seq
Using alternative normalization method in DESeq analysis of gene enrichment

I'm using DESeq to identify differentially expressed genes in a next-gen sequencing dataset. (DESeq: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3218662/). In my experiment, the normalization of read...
Forum: Sample Prep / Library Generation 04-30-2014, 02:53 AM
Replies: 0
Views: 1,015
Posted By simon_seq
Exclamation Debugging PCR-based amplification of mutant library

Dear all,
I've come across a rather odd case of PCR problems with a mutant library, which is used in directed evolution experiments. The library was made using site-directed mutagenesis, so that...
Forum: Clinical Sequencing 02-13-2014, 12:47 PM
Replies: 0
Views: 5,252
Posted By simon_seq
SNPs missing in HuGE Navigator

Hi all,
I really like HuGE Navigator's 'Gene Evidence' function where you can find all genes associated with a given disease, including a gene evidence score, which takes into account the numbers of...
Forum: Genomic Resequencing 02-10-2014, 06:24 AM
Replies: 2
Views: 1,818
Posted By simon_seq
Hi TiborNagy, Thanks for your quick reply. This...

Hi TiborNagy,
Thanks for your quick reply. This is good to know - in this case I will indeed move on to the cluster...

Best
Simon
Forum: Genomic Resequencing 02-10-2014, 03:11 AM
Replies: 2
Views: 1,818
Posted By simon_seq
1k genomes and VCF: slow processing of individual genome

Hi all,
I'm currently having troubles extracting a single genome's VCF file from the 1000 genomes repository. Theoretically using tabix and vcftools it's working, but it just appears to be...
Forum: Bioinformatics 04-09-2013, 03:33 AM
Replies: 2
Views: 1,234
Posted By simon_seq
Hi swbarnes2, Thanks for your reply. It's...

Hi swbarnes2,

Thanks for your reply. It's probably reasonable to suggest a more sensitive aligner. The reason I've chosen bowtie is its performance on large datasets, not requiring any...
Forum: Bioinformatics 04-08-2013, 10:13 AM
Replies: 2
Views: 1,234
Posted By simon_seq
Analyzing mutational bias in single gene

Hello,
I've got a small bioinformatics problem that I'm sure is easy for many of you to solve.

For my project I create mutant libraries of a gene. For instance within 300 nucleotides I have 5...
Forum: Illumina/Solexa 08-13-2012, 09:50 AM
Replies: 6
Views: 9,011
Posted By simon_seq
Well thank you all for your helpful and quick...

Well thank you all for your helpful and quick advice!

After reading your replies and calling Illumina I'm set to spike 40% PhiX for the next run and use 8 pM.

@zherbert: Agreed, I'll use 8 pM....
Forum: Illumina/Solexa 08-10-2012, 03:57 AM
Replies: 6
Views: 9,011
Posted By simon_seq
Need help debugging a faulty MiSeq run

Hi all,

I've just had a faulty MiSeq run and before I re-run my samples, I'd like to make sure the next run is going to be valid, especially since it's a rather expensive technique. It'd be great...
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