Dear all,
I am analyzing a dataset of RNA-seq (from Illumina Genome Analyser IIx), and have found some interesting expression pattern trends related to the GC content of genes. After reading the literature, I have noticed that RNA-seq has some biases related to the GC content. Hence, I am not sure of the validity of my inferences.
So, my question, or questions are:
-How can I determine if this is a biologically meaningful trend or rather so a bias of the methodology?
-To what extent does the GC content biases the results of RNA-seq experiments? (the "trends" that I observe are strong)
-I am working with published RPKM values, and was wondering if I need to recalculate all these values considering GC content biases or if I could just test how much bias is in the data.
Any clue with any of these questions is highly appreciated!
Federico
I am analyzing a dataset of RNA-seq (from Illumina Genome Analyser IIx), and have found some interesting expression pattern trends related to the GC content of genes. After reading the literature, I have noticed that RNA-seq has some biases related to the GC content. Hence, I am not sure of the validity of my inferences.
So, my question, or questions are:
-How can I determine if this is a biologically meaningful trend or rather so a bias of the methodology?
-To what extent does the GC content biases the results of RNA-seq experiments? (the "trends" that I observe are strong)
-I am working with published RPKM values, and was wondering if I need to recalculate all these values considering GC content biases or if I could just test how much bias is in the data.
Any clue with any of these questions is highly appreciated!
Federico
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