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Forum: Bioinformatics 06-15-2013, 11:45 AM
Replies: 5
Views: 2,947
Posted By john_nl
Most tools that test for differential expression...

Most tools that test for differential expression will account for this problem. For example, see the median count ratio method of the DESeq packages.
Forum: Bioinformatics 05-07-2013, 01:02 AM
Replies: 8
Views: 8,990
Posted By john_nl
DESeq Variance Stabilizing Transformation

Hello,

I am looking for some feedback regarding the use of the variance-stabilization (VST) methods found in the DESeq2 package. Hopefully one of the authors will respond and the comments will be...
Forum: Bioinformatics 04-11-2013, 12:04 PM
Replies: 2
Views: 1,757
Posted By john_nl
I would perform runs with width ranging from from...

I would perform runs with width ranging from from 6-8, 8-10 and 10-12. This is because MEME "likes" to discover the longest motif it can in my experience. Zoops mode is probably most sensible but...
Forum: Bioinformatics 01-17-2013, 10:15 AM
Replies: 1
Views: 887
Posted By john_nl
You could use the tool described here: ...

You could use the tool described here:
http://meme.nbcr.net/meme/fimo-intro.html
Forum: Bioinformatics 12-18-2012, 11:02 AM
Replies: 3
Views: 3,201
Posted By john_nl
Maybe it would be a good idea to analyze the...

Maybe it would be a good idea to analyze the distribution of intron lengths in the genome you study. Then pick the 95th percentile or something like that as the maximum intron size to avoid 'odd'...
Forum: RNA Sequencing 10-31-2012, 01:46 AM
Replies: 6
Views: 3,077
Posted By john_nl
The Upper Quartile normalisation method does just...

The Upper Quartile normalisation method does just essentially use the count value at the 75th percentile as the denominator.

Also, for people thinking about normalization methods I would recommend...
Forum: Bioinformatics 10-23-2012, 01:14 AM
Replies: 10
Views: 4,619
Posted By john_nl
I have a similar experimental set-up as above and...

I have a similar experimental set-up as above and therefore face the same decision. Essentially the question is, assuming > 2 samples (comparisons) should the variance estimation...
Forum: RNA Sequencing 07-26-2012, 05:14 AM
Replies: 6
Views: 3,077
Posted By john_nl
Glad i'm not the only one who thinks this. I'm...

Glad i'm not the only one who thinks this. I'm sure there is an explanation, but at the moment it does not seem intuitive to me.
Forum: Bioinformatics 07-05-2012, 01:21 AM
Replies: 1
Views: 1,988
Posted By john_nl
Tophat - reporting only best hit given multi-reads/multi-maps.

Hello,

Maybe someone has an answer regarding the issue of multi-reads/multi-maps with Tophat.

With Bowtie, parameters can be set such that it only reports alignments in the specified stratum...
Forum: Bioinformatics 02-22-2012, 05:37 AM
Replies: 1
Views: 2,051
Posted By john_nl
Analyzing expression time course with DESeq

Hello,

I have 11 samples covering 10 time points. Time point 1 has a control sample and a treated sample. The following 9 time points are all treated samples.

I wish to be able to compute the...
Forum: Bioinformatics 02-15-2012, 11:28 PM
Replies: 5
Views: 2,857
Posted By john_nl
Thank you very much for all of your answers. Much...

Thank you very much for all of your answers. Much appreciated.
Forum: Bioinformatics 02-13-2012, 06:29 AM
Replies: 5
Views: 2,857
Posted By john_nl
Combining FPKM values for a gene

Hello,

Hopefully this is a simple question that gets a simple answer:

I just want to map my reads using bowtie to a well defined transcriptome in the form of a cDNA library. This works very...
Forum: Bioinformatics 02-02-2012, 07:18 AM
Replies: 2
Views: 1,582
Posted By john_nl
Running problem with cuffdiff

Hello,

I have problem with cuffdiff, where it complains about the SAM file not been sorted correctly:

Error: this SAM file doesn't appear to be correctly sorted!
current hit is at...
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