Hello,
I have the RNA seq results (expressed as RPKM) of 8 samples: 1 set of control and 1 set of knock down for my gene of interest, all of the treated with 4 different cytokines.
Does anyone know what software I could use to:
- Sort the transcripts that are over/dow-regulated by the stimulations
- Identify which transcripts are sensible to the knock down of my favorite gene
One of my colleague suggested the "manual" option, but I don't really have the time :-)
Thanks
Hi, for your two-factor experiment (cell type, cytokine treatment), the best solution may be recent versions of edgeR. edgeR now allows more than one factor to be analyzed and is considered state-of-the-art. For more information, check the recent publication by McCarthy, Chen, and Smyth:
http://nar.oxfordjournals.org/content/early/2012/02/06/nar.gks042.abstract
Note, to use edgeR, you'd need the original count data (not RPKM). If you don't have the time to learn R (which is required to implement recent versions of edgeR), you could opt to analyze one factor at a time (say, a single cytokine treatment in w.t. vs knockdown) and use this web implementation of edgeR or another tool:
http://www.ijbcb.org/DEB/php/onlinetool.php
Cheers,
Stewart
Hi, for your two-factor experiment (cell type, cytokine treatment), the best solution may be recent versions of edgeR. edgeR now allows more than one factor to be analyzed and is considered state-of-the-art. For more information, check the recent publication by McCarthy, Chen, and Smyth:
http://nar.oxfordjournals.org/content/early/2012/02/06/nar.gks042.abstract
Note, to use edgeR, you'd need the original count data (not RPKM). If you don't have the time to learn R (which is required to implement recent versions of edgeR), you could opt to analyze one factor at a time (say, a single cytokine treatment in w.t. vs knockdown) and use this web implementation of edgeR or another tool:
http://www.ijbcb.org/DEB/php/onlinetool.php
Cheers,
Stewart
Hi! Use the suggestions above for a first iteration, but them check it manually, for sure the sottware will exclude some data that should be part of your data set (you shoul go for high-stringency). Is far better to miss out some data (even manually) than to include in your data set false positive.
Sorry couldn't be more helpfull.
Good luck!
CGR
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