|
|
Depth of Sequencing Normalization
This step estimates the depth of sequencing to compare two different samples. For example, if the average counts of nondifferentially expressed genes in one sample are twice as high as in another sample, the depth of sequencing for the first sample is twice that of the other sample.
For each transcript, the geometric mean of aligned read counts is calculated for all sample IDs. The median of the ratio of raw counts to the geometric mean is used as the scaling factor for each replicate. When evaluating nondifferentially expressed transcripts, dividing raw counts by the scaling factor yields equivalent scaled counts. By default, the expression levels for each replicate are normalized based on the total number of aligned reads.