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Forum: Epigenetics 05-11-2009, 10:36 PM
Replies: 20
Views: 63,532
Posted By Chema
Hi, In this paper, you can find other...

Hi,

In this paper, you can find other ChIP-seq algorithm. It is implemented in R
http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2671559

The baisc idea was
1) Extend the reads and...
Forum: 454 Pyrosequencing 04-09-2009, 05:50 AM
Replies: 10
Views: 9,379
Posted By Chema
Perhaps this paper can help you: ...

Perhaps this paper can help you:
http://genomebiology.com/content/pdf/gb-2007-8-7-r143.pdf
Forum: Epigenetics 12-03-2008, 02:40 AM
Replies: 8
Views: 3,313
Posted By Chema
Hi, In our ChIP-Seq experiments we also see...

Hi,

In our ChIP-Seq experiments we also see something similar. Not sure why. But in our case they are strand dependent (they pile up in some short region but only mapping to one strand), so what...
Forum: Bioinformatics 10-10-2008, 06:45 AM
Replies: 52
Views: 81,309
Posted By Chema
Hi Victor, What I wanted to say is that if...

Hi Victor,

What I wanted to say is that if you have a group of genes that are less expressed in condition 2 than 1, then, you will have less reads that represent these genes in condition 2 than 1,...
Forum: Bioinformatics 09-23-2008, 04:26 AM
Replies: 52
Views: 81,309
Posted By Chema
Hi, The point with RPKM that I do not like,...

Hi,

The point with RPKM that I do not like, it is that I do not feel that it can handle different coverages. Perhaps I can explain it better through an example.

Let say that we are working with...
Forum: Bioinformatics 09-22-2008, 02:11 AM
Replies: 52
Views: 81,309
Posted By Chema
What we are doing is to apply kind of quantile...

What we are doing is to apply kind of quantile normalization. After to obtain a score for each miRNA , since we are expecting that most of the miRNA have similar expression in both tissues at study,...
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