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In RNA-seq data analysis, after alignment, the most common step is to estimate gene or/and transcript expression abundance, the expression level is represented by read counts. There are three options in this step:
- Quantify to annotation model (Partek E/M)
- Quantify to transcriptome (Cufflinks)
Quantify to reference (Partek E/M)
The three options will be discussed below.
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