Hi,

I am working on RNA-seq data (Solid) which contains 2 sample groups and each group contains 5 biological replicates. I am interested in finding the differentially expressed genes between these 2 groups. I want to use cuffdiff for this purpose. However, I have certain questions:

1) Does cuffdiff find differentially expressed genes between the groups or across the replicates?

2) Data can be normalized using the option -N (upper quartile normalization). I believe it carries out within sample normalization but what about sample to sample normalization? Does cuffdiff carries out sample to sample normalization before comparing the groups?

Can anyone kindly answer these questions?

Thank you

I am working on RNA-seq data (Solid) which contains 2 sample groups and each group contains 5 biological replicates. I am interested in finding the differentially expressed genes between these 2 groups. I want to use cuffdiff for this purpose. However, I have certain questions:

1) Does cuffdiff find differentially expressed genes between the groups or across the replicates?

2) Data can be normalized using the option -N (upper quartile normalization). I believe it carries out within sample normalization but what about sample to sample normalization? Does cuffdiff carries out sample to sample normalization before comparing the groups?

Can anyone kindly answer these questions?

Thank you

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