# 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)](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/quantification/quantify-to-annotation-model-partek-em)
* [Quantify to transcriptome (Cufflinks)](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/quantification/quantify-to-transcriptome-cufflinks)
* [Quantify to reference (Partek E/M)](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/quantification/quantify-to-reference-partek-em)
* [Quantify regions](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/quantification/quantify-regions)
* [HTSeq](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/quantification/htseq)
* [Count feature barcodes](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/quantification/count-feature-barcodes)
* [Salmon](https://help.connected.illumina.com/partek/partek-flow/user-manual/task-menu/quantification/salmon)