Quantification

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)

• Quantify regions

• HTSeq

• Count feature barcodes

• Salmon